Inheritance Part I: Solving Genetic Problems (Summary)

Results of genetic crosses that obeys Mendel's Laws involves genes that are un-linked Crosses that do not obey Mendel's law involve linked genes
Monohybrid Inheritance: Mendel's 1st law of segregation applies Mendel's 2nd Law of independent assortment Linkage
Involves 1 character, 1 gene on a single pair of homologous chromosome 2 characters, 2 genes on 2 different pairs of chromosomes 2 characters, 2 genes on the same chromosome
Autosomal Inheritance Sex-linked Inheritance Dihybrid Inheritance Two types of linkage
Fixed genetic ratio Involves only sex chromosomes, or Fixed ratios Complete no Fixed ratios Incomplete with crossing over
Types of crosses Types of crosses
Genotypic Phenotypic specifically X chromosome genotypic Phenotypic crossing over Genotypic Phenotypic will result in

Complete Dominance Reciprocal cross results are non- Complete Dominance

identical when traits are reversed LG lg
X All dominant All dominant
Aa X Aa 1:2:1 3:1 for parents of different gender AaBb X AaBb Too many 9:3:3:1 LG lg
combinations
AA X aa (test cross) All dominant Inheritance adopts the following to narrow
pattern: down to fixed No fixed ratios
Aa X aa (test cross) 1:1 1:1 ratios LG LG Parental phenotypes
X 1:2:1 3:1
- Fathers pass X-linked alleles only lg lg (majority)
to daughters Recombinant phenotype
Incomplete Dominance Test cross (minority)
- Sons receive X-linked alleles only Test cross
R W R W
C C X C C 1:2:1 1:2:1 from mothers AABB X aabb All dominant LG lg No fixed ratios
X 1:1 1:1
lg lg Parental phenotype
All intermediate phenotype (majority); Recombinant
CRCR X CWCW phenotype (minority)
There are no fixed genetic ratio AaBb X aabb 1:1:1:1
for results of crosses
CRCW X CWCW 1:1 1:1
Only 2 types of gametes as the two genes 4 types of gametes
R W R R
C C X C C 1:1 1:1 are linked as one can be produced due
to crossing over
Codominance Key: ( 2 parental types;
- Capital letters denote dominant alleles 2 recombinant)
CRCW X CRCW 1:2:1 1:2:1 - small letters denote recessive alleles
- eg. AA (homozygous dominant), aa (homozygous recessive)
Both phenotypes equally
Aa (heterozygous at 1 gene loci)
CRCR X CWCW
expressed
Link concepts here to relevant topics:
1. Gene expression Knowledge of results of genetic cross can be used in
R W W W
C C X C C 1:1 1:1 - how genotype determine phenotype chromosome mapping
2. Cell and nuclear division
CRCW X CRCR 1:1 1:1 - how meiosis result in genetic variation
Number of recombinants (offspring)
COV = X100%
Lethal genes (Yy x Yy) 1:2:1 2:1 Total number of offsprings

Multiple alleles No fixed ratios To determine: } Increase in distance >> increase

(i) Distance between linked genes } number of recombinant
Knowledge of results of genetic crosses can be used to solve problems regarding Pedigree analysis (ii) Linear order of linked genes } phenotypes

If trend does not fit into any of the above, suspect:

1. Mutation (gene and chromosomal mutation)
2. Modification by the environment

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 INHERITANCE I
The chromosomal basis of inheritance sheds light on the pattern of transmitting genes from
parent to offspring

When Gregor Mendel first started his investigations into inheritance, the concept of genes had not
existed yet. He used the term ‘traits’ in place of genes. By using genetic diagrams, the phenotypic
and genotypic ratios of filial generations can be predicted for crosses involving monohybrid or dihybrid
inheritance. In line with Mendelian genetics, pedigree diagrams can be used to predict the probability
of inheriting genetic diseases such as haemophilia and Huntington’s disease.

Non-Mendelian inheritance involves more complex traits. For example, some genes are found on sex
chromosomes while others involve multiple alleles. For example, alleles of some genes exhibit co-
dominance or incomplete dominance and some genes have multiple alleles or are found on the sex
chromosomes. Furthermore, phenotype may depend on interactions between two or more genes, e.g.
epistasis. In addition, the inheritance of linked genes does not follow Mendelian laws; in predicting the
phenotypic and genotypic ratios of filial generations for linked genes, the occurrence and frequency of
crossing over has to be considered.

This concept includes both Mendelian and non-Mendelian inheritance. Besides genetics, the
environment also plays a role in determining the phenotype of an organism. Statistical tests, such as
the chi-squared test, allow scientists to test the significance of differences between observed and
expected results of genetic crosses.

LEARNING OUTCOMES
Candidates should be able to:

Core Idea 2
(u) explain the terms: locus, allele, dominant, recessive, codominant, incomplete dominance,
homozygous, heterozygous, phenotype, genotype and linkage
(v) explain how genes are inherited from one generation to the next via the germ cells or gametes
(w) explain how genotype is linked to phenotype
(x) use genetic diagrams to solve problems in dihybrid crosses, including those involving
codominance, incomplete dominance, multiple alleles, sex linkage, autosomal linkage and
epistasis
(y) use genetic diagrams to solve problems involving test crosses
(z) explain the meaning of the terms linkage and crossing-over and explain the effect of linkage and
crossing-over on the phenotypic ratios from dihybrid crosses
(bb) explain, with examples, how the environment may affect the phenotype (including how diet affects
the differentiation of honey bees and how temperature affects fur colour of Himalayan rabbits)

Use the knowledge gained in this section in new situations or to solve related problems.

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 LEARNING EXPERIENCES

Gregor Mendel’s study of inheritance can be linked to the Thomas Hunt Morgan’s chromosome theory
of inheritance: Morgan confirmed the Mendelian laws of inheritance and the hypothesis that genes are
located on chromosomes. Of great significance is that Mendelian genetics (together with population
genetics and molecular DNA) provided natural selection with the mechanism in Charles Darwin’s
theory of evolution (which Darwin was not aware of in his time).

Huntington's disease could be used as an autosomal dominant condition to help students differentiate
the concepts of ‘autosomal’ from ‘sex-linked’ and ‘dominant’ from ‘recessive’.

Examples using the ABO blood group and snapdragon flower colour could be used to distinguish
codominance from incomplete dominance respectively.

The concept of sex linkage and the implications of the gene for eye colour (red-white) in fruit flies to
be found on a locus on the X chromosome can be illustrated with Thomas Hunt Morgan’s experiments
with the fruit flies. Morgan was the first person to demonstrate through experimentation, that one gene
can be isolated to one chromosome. Morgan was awarded the Nobel Prize in 1933 for his work on
fruit flies. Online animations are available to explain how he determined that the gene coding for eye-
colour was located on the X chromosome.

REFERENCES

1. Biology: A Global Approach, 10th Ed. (2015). Campbell N. A. et al. Pearson.

2. Concepts of Genetics, 8th Ed. (2006). Klug WS, Cummings MR and Spencer. CA.
3. An Introduction to Genetic Analysis, 8th Ed. (2006). Anthony J. F. Griffiths. W. H. Freeman.
4. Essentials of Genetics, 7th Ed. (2010). William S.K. et al. Pearson.
5. Introduction to Advanced Biology. (2000). Clegg C. J. London: John Murray.

WEBSITE RESOURCES

S/N QR Code Website

Gregor Mendel and the Principles of Inheritance

1. http://www.nature.com/scitable/topicpage/gregor-mendel-and-the-
principles-of-inheritance-593

Genetics: Online Learning Center

2. http://highered.mheducation.com/sites/0072919345/student_view0/chapter
11/elearning.html#

Genetic inheritance follows rules

3.
http://www.dnaftb.org/5/

Genetics Animations
4.
http://bio-alive.com/animations/genetics.htm

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 LECTURE OUTLINE

1. Introduction to Genetics 4
2. Genetic Terminologies 5
2.1 Link between Genotype and Phenotype 6

3. Mendel's Breeding Experiments 7

4. Monohybrid Inheritance 8
4.1 Monohybrid Cross 10
4.2 Mendel's First Law of Segregation 10
4.3 Reciprocal Cross 11
4.4 Test Cross 11

5. Modifications of Classical Monohybrid Inheritance 12

5.1 Incomplete Dominance 12
5.2 Codominance 13
5.3 Multiple Alleles 15
5.4 Lethal Genes 17

6. Dihybrid Inheritance 18
6.1 Dihybrid Cross 18
6.2 Mendel's Second Law of Independent Assortment 19
6.3 Test cross 20

CONCEPT CHECK 1

7. Sex-linked Inheritance 23
7.1 Sex Determination in Human 23
7.2 Human X-Linked Disorders 24
7.3 Reciprocal Cross 27
8. Pedigree Analysis 28
8.1 Autosomal Recessive Inheritance 30
8.2 Autosomal Dominant Inheritance 30
8.3 X-Linked Recessive Inheritance 31
8.4 X-Linked Dominant Inheritance 32
9. Linkage 33
9.1 Complete Linkage 34
9.2 Incomplete Linkage 37
9.3 Detection of Linkage 39
9.4 Chromosome Mapping 40

CONCEPT CHECK 2

10. Phenotypic Variance 46

10.1 Effect of Genotype on Phenotype 46
10.2 Effect of Environment on Phenotype 47

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 1. INTRODUCTION TO GENETICS
GENETIC TERMINO
In 1866, Gregor Johann Mendel published the
results of a series of experiments that would lay
foundation for the formal discipline of genetics.
Mendel is known as the ‘Father of Genetics’.

When Mendel began his studies of inheritance

using Pisum sativum, the garden pea,
chromosomes and the role of and mechanism of
meiosis were totally unknown. Nevertheless, he
determined that discrete units of inheritance
exist and predicted their behavior during the
formation of gametes.

Genetics is the specialised branch of biology concerned with the study of heredity and variation
among individuals related by descent.

Heredity • Transmission of genetic characteristics from one generation to the next and the
effects of this transmission.

Variation • The recognisable differences between individuals of the same species and
between parents and offsprings.

Mendel uses a Model Experimental Approach to study Patterns of Inheritance

Practices of Science:
Demonstrating Science Inquiry Skills
• Identify scientific problems, observe phenomena and pose scientific questions / hypotheses
• Plan and conduct investigations by selecting the appropriate experimental procedures,
apparatus and materials, with due regard for accuracy, precision and safety
• Obtain, organise and represent data in an appropriate manner
• Analyse and interpret data
• Construct explanations based on evidence and justify these explanations through sound
reasoning and logical argument

Mendel showed remarkable insight into the methodology necessary for good experimental biology.
He chose an organism that is easy to grow and hybridise artificially. The pea plant is self-fertilising
in nature but is easy to cross-breed experimentally. It reproduces well and grows to maturity in a
single season.

Mendel followed seven visible features (unit characters), each represented by two contrasting forms
or traits (Fig. 1).

There were several reasons for Mendel’s success. In addition to his choice of a suitable organism, he
restricted his examination to one or very few pairs of contrasting traits in each experiment. He also
kept accurate quantitative records, a necessity in genetic experiments. From the analysis of his
data, Mendel derived certain postulates that became principles of transmission genetics.

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 2. GENETIC TERMINOLOGIES

1. Gene • A unit of inheritance located at a particular locus of a chromosome.

• A specific DNA nucleotide sequence which codes for RNA (mRNA, tRNA
or rRNA) or a polypeptide.

2. Locus • The specific location of a gene on a chromosome.

(plural: loci)

3. Allele • An alternative form of a gene at a particular gene locus.

• Responsible for determining contrasting traits of the same character.
• All alleles of a gene determine the same character, but each has a unique
DNA nucleotide sequence, which may result in different phenotypes.
• Alleles occur in pairs in a diploid cell although only one of the pair is
represented in a gamete.

Genotype

Tt

Ee

FF

Gg

hh

Fig. 1: Relationship between homologous chromosomes, gene loci and alleles.

4. Genotype • The complete genetic makeup / allelic composition of an organism.

• The term is also commonly used in reference to the paired alleles carried
by an organism that give rise to a phenotype.

5. Phenotype • The physical manifestation of a genetic trait that results from a specific
genotype and its interaction with the environment.

6. Wild-type • The most common allele / phenotype in nature.

7. Homozygous • Condition in which the alleles of a gene pair in diploid condition are
identical, e.g. TT or tt, where T is the dominant allele for tall stem and t is
the recessive allele for short stem.
• An organism with this condition is known as a homozygote and referred
to as true or pure breeding. All gametes produced by this organism will
carry the same allele.

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 8. Heterozygous • Condition in which the alleles of a gene pair in diploid condition are
different, e.g. Tt.
• An organism with this condition is known as a heterozygote. 50% of its
gametes will carry one allele while the other 50% will carry the other allele.

9. Dominant • Produce their effects in both homozygous and heterozygous condition

Alleles i.e. one copy of the allele is sufficient to cause the organism to express the
phenotype it encodes, e.g. allele T causes the plant to be tall in either TT
or Tt condition.
• A dominant allele masks the influence of the recessive allele.
• An organism homozygous for a dominant allele is known as homozygous
dominant.

10. Recessive • Produce their effects only in homozygous condition, e.g. allele t causes
Alleles the plant to be short only in the tt condition.
• An organism homozygous for a recessive allele is known as homozygous
recessive.

11. True- • An organism that gives rise to all offspring of the same phenotype i.e.
breeding organism is homozygous.

12. Carriers • A person or other organism that has inherited a recessive allele for a
genetic trait or mutation but does not display that trait or show
symptoms of the disease.

2.1 LINK BETWEEN GENOTYPE AND PHENOTYPE

Alleles being alternative or different forms of a gene are transcribed to form mRNA and translated
into different polypeptide chains and proteins which may affect different metabolic pathways resulting
in formation of different phenotypes. Each allele thus specifies or codes for the specific 3D
conformation of a particular protein which directly determines a trait, such as in this case having
either tall or dwarf stem.

A genotype is the genetic makeup of an organism, which refers to the paired alleles that produces a
phenotype which is a measurable or distinctive character, an example being the stem height of pea
plants.

In the pea plant with tall stem, when the genotype of the organism consists of either one or two
copies of the dominant allele of the gene for stem height, the plant displays a phenotype of tall
stem, as a result of the presence of a protein which contributes to growth of stem.

If the genotype lacks a dominant allele or consists of two copies of recessive alleles of the gene
for stem height, the plant display a phenotype of dwarf stem as a result of the lack of the protein
which contributes to growth of stem.

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 3. MENDEL’S BREEDING EXPERIMENTS

Mendel selected seven characters to study in the breeding experiments (Fig. 2). For each character,
he cross-pollinated two contrasting, true-breeding pea varieties.

Fig. 2: Seven pairs of constrasting traits and the results of Mendel’s seven monohybrid crosses of the garden pea
(Pisum sativum). In each case, pollen derived from plants exhibiting one trait was used to fertilise the ova of plants exhibiting
the other trait. In the F1 generations, one of the two traits was exhibited by all plants. The contrasting trait reappeared in
approximately ¼ of the F2 plants.

Summary of important terms from Mendel’s breeding experiments:

• The mating or crossing of two true-breeding varieties is called hybridisation.
• Each variant for a character had two distinctive, alternative appearances ie. phenotypes.
• The true-breeding parents are referred to as the P generation (parental generation).
• Their hybrid offspring are known as the F1 generation i.e. first filial generation.
• Self-pollination of F1 produces an F2 generation i.e. second filial generation.

From the patterns of inheritance that he observed, Mendel formulated two laws:
Mendel’s laws of inheritance:
1. Mendel’s First Law of Segregation
2. Mendel’s Second Law of Independent Assortment

Both laws could be related to the behavior of chromosomes during meiosis.

Mendel’s First Law of Segregation is based on his work involving monohybrid crosses i.e.
Monohybrid inheritance.

Mendel’s Second Law of Independent Assortment is based on his work involving dihybrid crosses
i.e. Dihybrid inheritance.

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 4. MONOHYBRID INHERITANCE

Mendel’s earliest experiments involved the study of only one character. The inheritance of a single
character of contrasting traits, e.g. tall stem vs short stem, is known as monohybrid inheritance.

The character is controlled by a single gene (a pair of alleles). It is studied by a cross between two
pure breeding organisms, which differ in one character. Such a cross is called a monohybrid cross.

4.1 MONOHYBRID CROSS

To fully understand the outcome and significance of the monohybrid cross, we have to construct a
genetic diagram.

Step Genetic Diagram

1 Define alleles Let T represent the dominant allele for tall stem
and t represent the recessive allele for dwarf stem
Note: Not needed if alleles are
already defined in question.

2 List down the parental Parental phenotype Tall Dwarf

phenotype and genotype

Each true-breeding plant of the Parental genotype TT x tt

parental generation has matching
alleles, TT or tt.

3 List down the parental Parental gametes T t

gametes
*Gametes should always
be circled
Each gamete contains only one
allele for the stem-length gene. In
this case, every gamete produced
by one parent has the same
allele.

4 List the F1 phenotype and F1 genotype All Tt

genotype using a Punnett F1 phenotype All tall
square (if necessary)

5 List the F1 gametes F1 phenotype Tall Tall

When the F1 hybrid plants
produce gametes, the two alleles F1 genotype Tt x Tt
segregate, with half the gametes
receiving the T allele and the
other half receiving the t allele. F1 gametes T t T t

6 List the F2 genotypes Random fertilisation

using a Punnett square
F1 Male gametes
The Punnett square shows all
possible combinations of alleles
in offspring. Each square T t
represents an equally probable
product of fertilisation.
F1 Female

T
gametes

TT Tt

t Tt tt

7 List the F2 genotypic and

phenotypic ratio F2 genotypic ratio 1TT : 2Tt : 1tt
Note: It is important to show
correlation between genotype & F2 phenotypic ratio 3 tall : 1 dwarf
phenotype.

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 Mendel’s Postulates and Explanations

1. Alleles come in Pairs

Genetic characters are controlled by alleles existing in pairs in individual organisms.

• In the monohybrid cross involving tall and dwarf plants, a specific allele, T and t exists for
each trait respectively.
• Each diploid individual receives one allele from each parent.
• As the alleles occur in pair, 3 combinations are possible:
- 2 factors for tallness, TT (homozygous)
- 2 factors for dwarfness, tt (homozygous)
- 1 of each factor, Tt (heterozygous).
• Every individual possesses one of these three combinations, which determine stem height.

2. Dominance or Recessiveness
While two unlike alleles responsible for a single character are present in a single individual,
one allele is dominant to the other, which is said to be recessive.

• In the monohybrid cross, the trait tall stem expressed in the heterozygous (Tt) F1 generation
results from the presence of the dominant allele, T.
• The trait dwarf stem not expressed in the F1 generation, but which reappears in the F2
generation, is under the influence of the recessive allele, t.
• In the F1 generation, the recessive allele, t for dwarf stem is masked by the dominant allele,
T for tall stem.
• The recessive allele, t is only able to express itself in the outward appearance of the plant
in the absence of the dominant allele, T as evident in the homozygous recessive (tt) F2
dwarf plants.
• The trait tall stem is dominant to the recessive trait, dwarf stem.

3. Segregation (Next section)

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 4.2 MENDEL’S FIRST LAW OF SEGREGATION

Mendel’s third postulate forms the basis of his First Law of Segregation.

Mendel’s First Law of Segregation:

During the formation of gametes, the paired alleles segregate randomly so that each gamete
receives one or the other with equal likelihood.

• Genes occur in pairs, with each being located on one of the pair of homologous chromosomes
in a diploid organism.
• When the pair of homologous chromosomes segregate from each other during anaphase I of
meiosis, they take their genes with them, resulting in each gamete receiving only one of each type
of chromosome (either the paternal or maternal chromosome), and thus one allele instead of the
normal two as shown in Fig. 3.

Fig. 3: Mendel’s First Law of Segregation is a result of meiosis.

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 4.3 RECIPROCAL CROSS

It is important to point out one further aspect of the monohybrid crosses. The F1 and F2 patterns of
inheritance are similar regardless of which parental plants served as the source of pollen (sperm) and
which served as the source of the ovum (egg).

The crosses could be made either way i.e. pollen from the tall plants pollinating dwarf plants, or vice
versa. These are called reciprocal crosses. Therefore, results of Mendel’s monohybrid crosses were
not sex dependent (KIV: Section 7.3).

4.4 TEST CROSS

Tall plants produced in the F2 generation are predicted to have either TT or Tt genotypes. To
distinguish the genotype of a F2 plant expressing the dominant phenotype of tall stem, a test cross
can be performed as shown in Fig. 4.

Purpose:
This involves crossing the organism of the dominant phenotype but unknown genotype with a
homozygous recessive individual. The phenotype of the offspring indicates the genotype of the
organism tested.

• If the organism displaying a dominant phenotype is homozygous, all the offspring will express the
dominant phenotype.
• However, if it is heterozygous, about half of the offspring will express the dominant phenotype
while the other half expresses the recessive phenotype in a 1: 1 ratio.

Fig. 4: Test cross of a single character. In (a), the tall parent is homozygous. In (b), the tall parent is heterozygous. The
genotype of each tall parent can be determined by examining the offspring when each is crossed to the homozygous
recessive dwarf plant.

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 5. NON-MENDELIAN INHERITANCE:
MODIFICATIONS OF CLASSICAL MONOHYBRID INHERITANCE

Mendel studied characteristics of pea plants which were determined by genes with an allele completely
dominant over the other form. However, gene expression is not limited to the complete dominance and
recessive model.

Sometimes, two different alleles collectively express their effects on the phenotype of an organism.

Modified F2
Examples
phenotypic ratio Results produced are different from that of
5.1 Incomplete dominance 1:2:1 Mendel’s experiments, i.e. there will be
modifications of the classical 3:1 ratio for
5.2 Codominance 1:2:1
the F2 generation for monohybrid
5.3 Multiple alleles No fixed ratio inheritance.
5.4 Lethal genes 2:1

5.1 INCOMPLETE DOMINANCE

Contrary to the Mendelian crosses discussed in Section 4, a cross between parents with contrasting
traits may sometimes generate offspring with intermediate phenotype. For example, if plants such as
snapdragons with red flowers are crossed with their counterparts with white flowers, the offspring
have pink flowers as shown in Fig. 5. Such a situation is known as incomplete dominance.

Incomplete • a condition where neither of

dominance the two alleles is
completely dominant to the
other, so that the
heterozygote has a
phenotype which is
intermediate.
• e.g. pink flowers between the
two homozygous forms (red
and white).

Flower colour in snapdragons is controlled by two alleles

of a flower-colour gene:
• Homozygotes for the red-flower allele (CRCR) have
red flowers.
• Homozygotes for the white-flower allele (CWCW)
have white flowers.
• Heterozygotes (CRCW) have pink flowers.

Fig. 5: Incomplete dominance in snapdragon flower colour.

When a trait exhibits incomplete dominance:

• A cross between two heterozygotes in F1 generation as shown in Fig. 5 produces a 1:2:1
phenotypic ratio in the F2 progeny.
• The 1:2:1 genotypic ratio for the F2 generation is identical to that of Mendel’s monohybrid crosses.
• Main difference from Mendel’s classical monohybrid crosses – Phenotypic ratio is identical
to the genotypic ratio.

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Biochemical Basis

Incomplete dominance in the heterozygote of snapdragons can be explained by postulating that the
allele CR allows the production of a functional enzyme required for the synthesis of red pigment.

Copy of allele / Amount of red pigment

Genotype Flower colour
enzyme produced (%)
Homozygote (CRCR) 2 100 Red
Homozygote (CWCW) 0 0 White
R W
Heterozygote (C C ) 1 50 Pink

Heterozygotes possess only one copy of the allele per cell and hence produces insufficient enzyme
to synthesise enough red pigment as compared to a homozygote CRCR that makes twice as much of
the red pigment. Consequently, the heterozygotes are pink. The allele CW codes for a non-functional
enzyme.

5.2 CODOMINANCE

Codominance • a phenomenon in which both alleles are equally expressed in the

phenotype of the heterozygote
• The heterozygote simultaneously expresses the phenotypes of both types
of homozygotes.

An example of codominance is the coat colour of short horn cattle. A cross between homozygous
red shorthorn cattle and homozygous white shorthorn cattle results in heterozygous offspring
with a roan coat. The roan coat consists of a mixture of all red hairs and all white hairs. As each hair
is either all red or all white, the condition is codominance. A subsequent cross between the roan
offspring results in offspring of all three coat colour.

Let CR represent the allele for the production of red hair

and CW represent the allele for the production of white hair

Parental phenotype Red coat colour White coat colour

Parental genotype CRCR x CWCW
Parental gametes CR CW
F1 genotype All CRCW
F1 phenotype All roan coat colour

F1 genotype CRCW x CRCW

F1 gametes CR CW CR CW

Random
Male gametes
fertilisation

CR CW\

CR CRCR CRCW
Female
gametes
CRCW CWCW
CW

F2 genotypic ratio 1 CRCR : 2 CRCW : 1 CWCW

F2 phenotypic ratio 1 red coat : 2 roan coat : 1 white coat

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Biochemical Basis

Both alleles of the hair-colour gene code for

functional products. Both products appear
in the phenotype of the heterozygote.

In this example, a heterozygote with roan coat

consists of a mixture of red hairs and white
hairs (Fig. 6).

Fig 6: Roan coat cows.

How to distinguish codominance from incomplete dominance:

For incomplete dominance, the heterozygote phenotype is intermediate between the two
homozygote phenotypes (e.g. pink flower versus red / white flowers).

For codominance, the heterozygote phenotype is NOT intermediate e.g. we do not get pink hair
cattle from breeding red and white cattle between the homozygote phenotypes. Instead, the
heterozygote possesses both parental traits in equal expression i.e. coat with a mixture of hairs
that are either completely red or completely white.

Another example of codominance is the MN blood group system in humans.

The MN system is under the control of a gene, L found on chromosome 4, with two codominant
alleles designated LM and LN which are responsible for the production of antigens M and N respectively
in human blood cells.

As predicted, a mating between two heterozygous MN parents may produce children of all three blood
types.

Let LM be the allele for the production of antigen M

and LN be the allele for the production of antigen N

Parental phenotype Blood group MN Blood group MN

Parental genotype LMLN x LMLN
M
Parental gametes L LN LM
LN

Random
Male gametes
fertilisation

LM LN

LM LMLM LMLN
Female
gametes
LN LMLN LNLN

Offspring genotypic ratio 1 LMLM : 2 LMLN : 1 LNLN

Offspring phenotypic ratio 1 M blood group : 2 MN blood group : 1 N blood group

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 5.3 MULTIPLE ALLELES

If a gene controlling a characteristic has three or more alleles, the alleles are called multiple alleles.
This is illustrated in the inheritance of the ABO blood groups in humans.

The ABO system, like the MN blood types, is characterised by the presence of antigens on surface
of red blood cells. However, the A and B antigens are distinct from the MN antigens and are under
the control of a different gene, located on chromosome 9.

The three alleles responsible for the production of antigens are designated IA, IB and i, where I / i
stand for isoagglutinogen, another term for antigen.

IA: allele for the production of antigen A

IB: allele for the production of antigen B
i: allele that produces neither antigens A or B

The IA and IB alleles are codominant to each other, while the i allele is recessive to both. Only two
of the three alleles can be present in an individual. Four possible blood groups but 6 possible
genotypes can result from various combinations of these three different alleles as shown below.

Phenotypes /
A B AB O
Blood Group
Genotypes IAIA, IAi IBIB, IBi I AI B ii

Example 1: Progeny of mating between individuals of blood group AB and group O

Parental phenotypes Blood group AB Blood group O

Parental genotypes IA IB x ii

Parental gametes IA IB i

Random Male gametes

fertilisation
IA IB
gametes
Female

IAi IBi
i

Offspring genotypic ratio 1 IAi : 1 IBi

Offspring phenotypic ratio 1 Blood Group A : 1 Blood Group B

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Example 2: Mating between heterozygous parents with blood groups A and B.

Parental phenotypes Blood group A Blood group B

Parental genotypes IAi x IBi

Parental gametes IA i IB i

Random Male gametes

fertilisation
IA i

IB

gametes
IAIB IBi

Female
i IAi ii

Offspring genotypic ratio 1 IAIB : 1 IAi : 1 IBi : 1 ii

Offspring phenotypic ratio 1 blood group : 1 blood group : 1 blood group : 1 blood group
AB A B O

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 5.4 LETHAL GENES

Countless gene products are essential for the survival of an organism. Mutations which lead to a non-
functional gene product can sometimes be tolerated in the heterozygous state. If a mutation results in
lethality, this is indicative that the affected gene has a fundamental function in the growth,
development and survival of an organism. Lethal genes can be recessive or dominant.

Recessive Lethal Genes

The snapdragon plant Antirrhinum with characterised condition aurea, has golden instead of green
leaves. When two aurea snapdragon plants were crossed, a 2:1 ratio of yellow seedlings to green
seedlings was observed. Homozygous aurea plants lack normal chlorophyll development and died
either during embryonic stage or when the plant seedlings were two to three days old.

Another example is a mutation that causes

yellow coat colour in mice. Coat colour in
mice is linked to a lethal gene.
Agouti

With regards to coat colour, the mutant yellow

allele Y is dominant to the wild-type agouti
allele y, hence heterozygous mice will have
yellow coats.

Cross breeding yellow mice (genotype Yy)

produces offspring in the ratio 2 yellow fur: 1
agouti fur as shown in Fig. 7. The atypical
Mendelian ratio is due to the fetal death of
homozygous yellow (YY) coat mice, so the
YY genotype is missing from the progeny.

Fig. 7: Effect of a lethal gene.

Animal homozygous for the wild-type y allele have yellow pigment deposited as a band on the
otherwise black hair shaft, resulting in the agouti phenotype. Heterozygotes deposit yellow pigment
along the entire length of hair shafts as a result of deletion of the regulatory region preceding the
DNA coding region of the Y allele. Without any means to regulate gene expression, one copy of the
Y allele is always turned on in heterozygotes, resulting in this gain of function leading to the
dominant effect.

Extensive deletion of genetic material characterizing the Y allele actually extends into the coding
region of an adjacent gene (Merc), rendering it non-functional. It is this gene that is critical to
embyronic development. Hence, this loss of function in YY homozygotes results in lethality.
Heterozygotes exceed the threshold level required of the wild-type Merc gene product.

Dominant Lethal Genes

Dominant lethal genes are expressed in both homozygotes and heterozygotes. They are rarely
detected due to their rapid elimination from populations. For example, Huntington’s disease, a
neurological disorder in humans, which reduce life expectancy. Since the onset of Huntington’s
disease is slow, individuals carrying the allele can pass it on their offspring.

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 6. DIHYBRID INHERITANCE

As a natural extension of the monohybrid cross discussed in Section 4, Mendel also designed
experiments in which he examined two characters simultaneously. The inheritance of two pairs of
contrasting characters in each cross is known as dihybrid inheritance.

6.1 DIHYBRID CROSS

A dihybrid cross is a genetic cross involving two characters in which the parents possess different
forms of each character. The two characters are controlled by two genes (2 pairs of alleles) located
on two gene loci on two different chromosomes.

For example, Mendel carried out crossing between true-breeding pea plants having yellow seeds
that were also round with those having green seeds that were also wrinkled. The procedure was
similar to what was discussed in Section 4.1.

Step 1
Let R represent the dominant allele for round seed,
r represent the recessive allele for wrinkled seed.
Y represent the dominant allele for yellow seed,
y represent the recessive allele for green seed.

Step 2
Parental phenotype Round and yellow seed Wrinkled and green seed
(homozygous) (homozygous)
Parental genotype RRYY x rryy

Step 3
Parental gametes RY ry

Step 4
F1 genotype All RrYy
F1 phenotype All double heterozygous round and yellow seed

Step 5
F1 phenotype Round and yellow seed Round and yellow seed
F1 genotype RrYy x RrYy

F1 gametes RY Ry rY ry RY Ry rY ry

Step 6
Random fertilisation (as shown in a Punnett Square)
F1 male gametes
RY Ry rY ry
RY RRYY RRYy RrYY RrYy
F1 Ry RRYy RRyy RrYy Rryy
female
rY RrYY RrYy rrYY rrYy
gametes
ry RrYy Rryy rrYy rryy

Step 7
F2 genotypic ratio 9R_Y_ : 3 R_ yy : 3 rr Y_ : 1 rryy

F2 phenotypic ratio 9 round yellow : 3 round green : 3 wrinkled yellow : 1 wrinkled green
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 6.2 MENDEL’S SECOND LAW OF INDEPENDENT ASSORTMENT

Mendel’s fourth postulate forms the basis of his Second Law of Independent Assortment.

Mendel’s Second Law of Independent Assortment

The segregation of one pair of alleles is independent of the segregation of other pairs.

• As a result of segregation, each gamete receives one member of each pair of alleles. For one pair,
whichever allele is received does not influence the outcome of segregation of any other pair. In
other words, each F1 gamete receives either a R or r allele and a Y or y allele.
• Independent assortment stipulates that all four combinations (RY, Ry, rY and ry) will be
formed with equal probabilities as shown in Fig. 8.

Fig. 8: Mendel’s Second Law of Independent Assortment is also a result of meiosis.

• It is important to note that this pattern of segregation would not occur if the genes were located
on the same chromosome, i.e. if they are linked genes.

Think: Explain why Mendel’s Second Law of Independent Assortment does not apply to linked genes
on the same chromosome.
Genes located close together on the same chromosome (linked genes) do not assort independently as they
are linked / joined together on the same chromosome (KIV: Section 9 Linkage). Note that independent
assortment involves the arrangement and separation of whole chromosomes and therefore all the alleles that
are on them will be moved together as one entity.

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 6.3 TEST CROSS

The expression of pea plants with round yellow seeds in the F2 generation might result from four
possible genotypes: RRYY, RRYy, RrYY and RrYy. To distinguish the genotype of a F2 plant
expressing the dominant phenotype of yellow round seeds, a test cross can be performed.

This involves crossing the organism that expresses the two dominant traits (round yellow seeds)
but unknown genotype with an individual which is homozygous recessive for both gene loci, i.e.
double homozygous recessive (wrinkled green seeds). The phenotype of the offspring indicates
the genotype of the organism tested.

Case 1 RRYY x rryy

Gametes RY

ry RrYy

All round yellow

Case 2 RrYy x rryy

Gametes RY Ry rY ry

ry RrYy Rryy rrYy rryy

1 round yellow : 1 round green : 1 wrinkled yellow : 1 wrinkled green

Case 3 RRYy x rryy

Gametes RY Ry

ry RrYy Rryy

1 round yellow : 1 round green

Case 4 RrYY x rryy

Gametes RY rY

ry RrYy rrYy

1 round yellow : 1 wrinkled yellow

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 CONCEPT CHECK 1

In Jimsonwood, purple flower is dominant to white and spiny pods are dominant to smooth. A true-
breeding plant with white flowers and spiny pods is crossed to a true-breeding plant with purple flowers
and smooth pods. Determine the phenotypic ratio of the:

(a) F1 generation
(b) F2 generation

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 SUMMARY OF *PHENOTYPIC RATIOS IN MONHYBRID & DIHYBRID CROSSES
* Distinguish between phenotypic and genotypic ratio

Monohybrid Crosses Phenotypic Ratio

All dominant
Homozygous dominant x Homozygous recessive
(heterozygous)
Heterozygote x Heterozygote 3:1

Heterozygote x Homozygous recessive (Test cross) 1:1

Heterozygote x Heterozygote in Incomplete Dominance / Codominance 1:2:1

2:1
Heterozygote x Heterozygote in Lethal genes
(¼ offspring dies)

Dihybrid Crosses Phenotypic Ratio

Double homozygous dominant (e.g. AABB) x Double homozygous All dominant

recessive (e.g. aabb) (Double heterozygous)

Double heterozygote (e.g. AaBb) x Double heterozygote (e.g. AaBb) 9:3:3:1

Double heterozygote x Double homozygous recessive (Test cross) 1:1:1:1

Think:
Mendel’s success was due to his careful choice of experimental organism, the garden peas, which
provided the following advantages:

1. The plant had varieties of distinct characteristics (discontinuous variation).

2. The peas were easy to cultivate.
3. They had a relatively short life cycle of one year.
4. The peas produced a large number of seeds.
5. Pollination of the pea plant was easy to control. Foreign pollen could be kept out and cross
fertilization could be accomplished artificially.
6. Pure breeds available.

Suggest why it is more difficult to investigate the patterns of inheritance in Man than in peas.

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 7. SEX-LINKED INHERITANCE

The results of Mendel’s monohybrid and dihybrid crosses as discussed in the earlier sections are
clearly not sex dependent. For this section, we will be looking at another mode of inheritance which
is linked to the sex of the organism.

7.1 SEX DETERMINATION IN HUMANS

Human Sex Chromosomes

There are 23 pairs of chromosomes in humans:

• First 22 pairs appear identical in both male and female. These chromosomes are known as
autosomes and are not involved in sex determination.
• The 23rd pair appears identical in the female (X chromosomes) but differs in the male (one X
chromosome and one Y chromosome). These are the sex chromosomes and are involved in
sex determination.

Production of Gametes & Sex Determination in Humans

• In humans, the female produces one type of gamete. All the egg cells carry an X chromosome.
Hence, the female is described as homogametic.
• In contrast, the male produces two types of gametes. Half of the sperm cells carry an X
chromosome while the other half carries a Y chromosome. The male is thus heterogametic.

The sex of an offspring is determined by the sperm that fertilises the egg cell as shown in Fig. 9.
• The egg cell may be fertilised by a sperm carrying an X chromosome:
- zygote produced will have two X chromosomes and will develop into a female.
• The egg cell is equally likely to be fertilised by a sperm carrying a Y chromosome:
- zygote produced will have one X chromosome and one Y chromosome, and will develop into
a male.

Fig. 9: Sex chromosomes are inherited in a normal Mendelian manner.

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Inheritance of Sex-Linked Genes in Humans

Sex linkage refers to the carrying of genes on the sex chromosomes. The genes are mostly located
on the X chromosome (rather than on the Y chromosome). The Y chromosome is shorter than the X
chromosome and carries very few genes as compared to the X chromosome. X chromosome contains
many loci that are required in both sexes, whereas the Y chromosome contains only a few genes.

Hence, genes located on the sex chromosomes, mainly the X chromosomes are known as sex-
linked genes or more appropriately X-linked genes because they follow the transmission pattern of
the X chromosome.

Examples of sex-linked inheritance include haemophilia, red-green colour blindness and Duchenne
muscular dystrophy in humans, and white eye colour in Drosophila.

The understanding of X-linked inheritance has helped elucidate how certain sex-linked characteristics
of interest (some of them linked to serious medical disorders) are transmitted from parents to offspring.

7.2 HUMAN X-LINKED DISORDERS

Several X-linked recessive disorders occur in humans including haemophilia, colour blindness
and Duchenne muscular dystrophy.

Before looking at them, it is important to understand the following:

1. Sex-linked Inheritance mainly affect Males

• As a male has only one sex-linked gene locus (1 copy of X chromosome instead of 2 as seen
in females), he is neither homozygous nor heterozygous for his sex-linked loci; instead he is
always hemizygous for every sex-linked locus (hemi means ‘half’).
• As males possess only a single X chromosome, whatever allele present on the X
chromosome of males will be directly expressed in the phenotype, whether or not if the
allele is dominant or recessive. Thus, X linked disorders mainly affect males as males are
hemizygous.

2. Representation of X-linked Alleles

• Designate X-linked alleles as superscripts on top of X or Y chromosomes in genetic
representation
• For example: For red–green colour blindness in humans,
Xb represents a X chromosome with a recessive allele for red–green colour blindness
XB represents a X chromosome with a normal dominant allele for normal colour vision.

• Females possess two X chromosomes; so there are three possible genotypes among females:
Both XBXB and XBXb result in normal vision, while XbXb results in colour blindness.
• Males have only a single X chromosome; so there are two possible genotypes: XBY results in
normal vision, while XbY results in colour blindness.

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 7.2.1 HAEMOPHILIA

Haemophilia refers to the reduced ability of blood to clot, due to deficiency of one of the blood clotting
factors.

It is caused by the X-linked recessive allele represented by h, while the normal dominant allele is
represented by H.

Worked Example

A female who is a carrier (heterozygote) of haemophilia marries a normal male.

Work out the genotype and phenotype of their offspring.

Let H represent the dominant allele for blood clotting,

h represent the recessive allele for haemophilia.

Parental phenotype Normal female (carrier) Normal male

Parental genotype XHXh x XHY
Parental gametes XH Xh XH Y

Random
Male Gametes
fertilisation

XH Y

XH XHXH XHY
Female Gametes
Xh XHXh XhY

Offspring genotypic ratio 1 XHXH : 1 XHY : 1 XHXh : 1 XhY

Offspring phenotypic ratio 1 normal : 1 normal : 1 normal : 1 haemophiliac
female male female male
(carrier)
Interpretation

Genotypes Phenotypes Comments

XHXH Normal female • In the female, the presence of a recessive allele for
haemophilia (h) can be masked by a dominant allele for
normal blood clotting (H). This type of individual is described
as a carrier (XHXh).
Normal carrier
XHXh
female • A carrier does not suffer from haemophilia, i.e. shows normal
blood clotting, but can transmit the recessive allele for
haemophilia to offspring.
XhXh Haemophiliac female
H
X Y Normal male
• In the male, the presence of a recessive allele for haemophilia
is sufficient to result in the disease because the Y
XhY Haemophiliac male
chromosome does not carry a dominant allele for normal
blood clotting to mask the recessive allele.

Conclusion

Haemophilia is more common in males than in females. This is because males need only one copy
of the defective recessive allele to suffer from haemophilia whereas females require two copies of
the defective recessive allele to be a sufferer.

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 7.2.2 RED-GREEN COLOUR BLINDNESS

Red-green colour blindness is the inability to distinguish between red and green.

It is caused by the X-linked recessive allele represented by b, while the normal dominant allele is
represented by B.

With reference to Fig. 10,

Let B be the dominant allele for normal

colour vision,

and b be the recessive allele for colour

blind vision.

Note:
The recessive allele for colour blindness
is passed from one sex to the other at
each generation.

The father passes it to his daughters

(but not his sons), who thus become
carriers.

The daughters in turn may pass it to

their sons, who are thus colour-blind.

Fig. 10: This pedigree for colour blindness exemplifies the

inheritance of an X-linked recessive disorder.

From the above examples, we can deduce some broad principles regarding sex-linked inheritance:
• An affected father will transmit the recessive X-linked allele to all daughters but not to any sons
because his son will inherit his Y chromosome only and the X chromosome from mother.

• If the mother is homozygous dominant, the daughters will have the normal phenotype but will be
carriers of the mutation i.e. they are heterozygous and have the ability to pass the recessive X-
linked allele to their offspring even though they do not express the recessive phenotype.

• Females who are heterozygous are described as carriers of the trait.

• If the carrier female marries with a normal male, there is a 50% chance that each daughter will
be a carrier like her mother, and a 50% chance that each son will have the disorder.

• It can thus be inferred that if the carrier female marries with an affected male, there is a 50%
chance that each child born to them will have the disorder, regardless of sex. Daughters who
do not display the recessive phenotype will be carriers, whereas males without the disorder will be
completely free of the recessive allele.

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 7.2.3 DUCHENNE MUSCULAR DYSTROPHY

This X-linked, recessive condition affects muscle development. Progressive weakness develops as
the muscles of the body are replaced by fibrous tissues. It is believed that the allele for DMD codes
for an enzyme that induces the replacement of muscle by fibre. A person with this disease rarely
survives beyond the age of 20.

The gene for DMD is sex-linked, and found on the X chromosome.

7.3 RECIPROCAL CROSS

Purpose: A reciprocal cross can be conducted to discern if a trait is carried on a sex chromosome
(X-linked) or on an autosomal chromosome. A reciprocal cross is a pair of crosses in which the traits
of the two parents are reversed. (Recall Section 4.3)

To determine if the locus for eye colour in Drosophila is on the X chromosome, the following crosses
are performed:
(a) Crossing a red-eyed male Drosophila with a white-eyed female Drosophila,
(b) Crossing a red-eyed female Drosophila with a white-eyed male Drosophila.

The allele for red eye is dominant to that for white eye.

Let R represent the dominant allele for red eye,

r represent the recessive allele for white eye.

Male (♂) or female (♀)

Cross 1: Red-eyed ♂ x White-eyed ♀
Cross 2: Red-eyed ♀ x White-eyed ♂

Cross between red-eyed male Reciprocal cross between homozygous red-eyed

and homozygous white-eyed female female and white-eyed male
XRY x XrXr XRXR x XrY
Random fertilisation Random fertilisation
Male gametes Male gametes
R
X Y Xr Y
gametes

gametes
Female

Female

Xr XRXr XrY XR XRXr XRY

Offspring genotype ratio 1 XRXr : 1 XrY Offspring genotype ratio 1 XRXr : 1 XRY
Offspring phenotype ratio 1 red- : 1 white- Offspring phenotype ratio 1 red- : 1 red-
eyed eyed eyed eyed
female male female male
Outcome: Outcome:
All males are white-eyed and all females are red- All offspring are red-eyed, regardless of sex.
eyed.

This is expected of X-linked genes, because

• the male transmits the X chromosome only to his female offspring,
• while the female transmits an X chromosome to both male and female offspring.
• Since the male parent does not transmit the X chromosome to his sons, he does not contribute to the
appearance of their X-linked phenotypes.
• Hence, reciprocal crosses involving X-linked traits yield non-identical results in contrast to reciprocal
crosses involving autosomal traits which yield identical results.

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 8. PEDIGREE ANALYSIS

In the study of human genetics, it is impossible to conduct breeding experiments. Studies must be
done using results of the matings that have already occurred: to study a family’s history for a particular
trait, and assemble the information into a pedigree chart.

A pedigree chart is a diagram of a family tree over as many generations as possible showing the
descendants from particular ancestors, their relationships and the presence or absence of the trait in
all the members as shown in Fig. 11.

Fig. 11: A simplified pedigree showing the X-linked inheritance of haemophilia in European royal families. As Queen
Victoria was a carrier, each of their four sons had a 50% chance of having the disorder, and each of her daughter has a 50%
chance of being a carrier. This pedigree shows only the affected descendents. Many others are unaffected, including the
members of the present British royal family.

By analysing a pedigree, we may be able to predict how the trait under study is inherited. This not
only helps us to understand the past; it also helps us to predict the future, e.g. in genetic counseling
and family planning. Fig. 12 shows the standard pedigree conventions.

Fig. 12: Symbols used in human pedigree analysis.

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Example 1: Inheritance of widow’s peak

Widow’s peak, a pointed contour of the hairline, is caused by the dominant allele, W. Individuals
with a widow’s peak are either homozygous dominant (WW) or heterozygous (Ww). On the other
hand, individuals who do not have a widow’s peak must be homozygous recessive (ww).

Analysis from Fig. 13a:

• The grandparents with a widow’s peak must be heterozygous as they produced offspring who
lacked widow’s peaks. Their offspring would all have widow’s peak if they are homozygous.
• The second generation individuals must be heterozygous as they have a parent who is a
homozygous recessive.

Example 2: Inheritance of attached earlobe

Attached earlobe is caused by the recessive allele, f.

Analysis from Fig. 13b:

• The first born daughter in the third generation (III-I) has attached earlobes although both parents
lack the trait.
• This explains the fact that the attached earlobe is due to a recessive allele and not to a dominant
allele.

Fig. 13: Pedigree Analysis. In these family trees, squares represent males and circles represent females. A horizontal
line connecting the male and female indicates a mating, with offspring listed below in their order of birth from left to right.

There are 4 main modes of inheritance which will be discussed in Sections 8.1 – 8.4:
8.1 Autosomal recessive
8.2 Autosomal dominant
8.3 Sex-linked recessive
8.4 Sex-linked dominant

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 8.1 AUTOSOMAL RECESSIVE INHERITANCE

• The gene of interest for the trait is carried on an autosome.

• A recessive trait only becomes phenotypically apparent when two similar alleles of a gene are
present. In other words, the subject must be homozygous for the trait.
• Fig. 14 illustrates a representative pedigree for a trait that demonstrates autosomal recessive
inheritance, such as albinism.

Fig. 14: Characteristics of an autosomal recessive inheritance.

Characteristics of an autosomal recessive inheritance

Recessive because:
1. If both parents are affected, all children should be affected.
2. In most cases, when unaffected people mate with affected individuals, all children are unaffected.
When at least 1 child is affected (indicating that the unaffected parent is heterozygous),
approximately half the children should be affected.
3. Unaffected parents (heterozygous at gene loci) can produce affected individuals.
4. Trait often skips generations.
Autosomal because:
1. Both males and females are affected with equal probability.

8.2 AUTOSOMAL DOMINANT INHERITANCE

• A single copy of the dominant allele is sufficient to allow the mutant phenotype to be expressed,
i.e. even if the individual is heterozygous.
• Fig. 15 illustrates a representative pedigree for a trait that demonstrates autosomal dominant
inheritance, such as Huntington disease.

Fig. 15: Characteristics of an autosomal dominant inheritance.

Characteristics of an autosomal dominant inheritance

Dominant because:
1. Unaffected parents should not have affected children.
2. Trait should not skip generations, i.e. affected individuals must have affected parent(s).
3. When an affected individual mates with an unaffected individual, 50% of their offspring should be
affected (indicating that the affected individual is heterozygous).
Autosomal because:
1. Both males and females are affected with equal probability.

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 8.3 X-LINKED RECESSIVE INHERITANCE

• The gene of interest for the trait is carried on the sex (usually X) chromosome.
• Males have only one X chromosome i.e. they are hemizygous for the trait, thus a single recessive
allele on the X chromosome will cause the male to display the disease phenotype. Hence, males
display disease phenotype more often than females.
• Females will require two recessive alleles, one on each of their X chromosomes, to display the
disease phenotype.
• Fig. 16 illustrates a representative pedigree for a trait that demonstrates sex-linked recessive
inheritance, such as haemophilia, colour-blindness and Duchenne Muscular Dystrophy as
discussed in Section 7.2.

Fig. 16: Pedigree showing sex-linked recessive alleles expressed in males. These alleles are carried unexpressed by
daughters in the next generation, to be expressed again in sons. Note that III-3 and III-4 cannot be distinguished
phenotypically.

Characteristics of a X-linked recessive inheritance

X-linked because:
1. Most affected individuals are males.
2. Affected mothers produce affected sons with 100% chance.
3. Affected females are the result of a mating between affected fathers and affected or carrier
mothers.
4. Approximately half of the sons of carrier females should be affected.

Recessive because:
1. If fathers are not affected, daughters will not be affected but may be carriers.

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 8.4 X-LINKED DOMINANT INHERITANCE

• The gene of interest for the trait is carried on the sex (usually X) chromosome. A single abnormal
allele on the X chromosome can cause a sex-linked dominant disease.
• Fig. 17 illustrates a representative pedigree for a trait that demonstrates sex-linked recessive
inheritance.

XaXa XAY

XaY XAXa XAXa XaY XaY

XaXa XAXa XaY XAY

Fig. 17: Pedigree of a sex-linked dominant condition. All the daughters of a male expressing a sex-linked dominant
phenotype will show the phenotype. Females heterozygous for a sex-linked dominant allele will pass the condition on to half
their sons and daughters.

Characteristics of a X-linked dominant inheritance

X-linked because:
1. Affected mothers produce affected sons (only 50% chance).
2. Affected females are the offspring of affected mothers or fathers.
3. All daughters, but none of the sons, of an affected father are affected, assuming mother is
normal (Refer to generation II).

Dominant because:
1. The trait does not skip generations.
2. Approximately half of the children of the affected heterozygote females are affected.

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 9. LINKAGE

In the early 1900s, genetic studies with several organisms revealed that certain genes were not
transmitted according to the law of independent assortment. Rather, these genes seemed to
segregate as if they were somehow joined or linked together. Further investigations showed that such
genes were part of the same chromosome, and they were transmitted as a single unit.

Linked • Genes that control different characters and situated on the same chromosome
genes at different loci

Recall in Section 6 on Dihybrid Inheritance, if both parents are homozygous at both gene loci and show
contrasting phenotypes, the phenotypic ratios of the F2 generation and of the test cross on the F1
generation are approximately 9:3:3:1 and 1:1:1:1 respectively. However, the two genes are unlinked,
i.e. located on different chromosomes and are hence distributed into gametes independently of
one another.

If the two gene loci are linked, then the ratios of 9:3:3:1 and 1:1:1:1 will not be observed.

Linked genes located on the same chromosome tend to be inherited together in genetic crosses
because the chromosome is passed together as a unit. Linked genes hence do not show
independent assortment and therefore fail to produce the expected 9:3:3:1 or 1:1:1:1 ratio in
breeding situation involving the inheritance of two pairs of contrasted characteristics.

The linkage of linked genes can be either complete or incomplete, depending on the relative
distance between each gene.

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 9.1 COMPLETE LINKAGE

In complete linkage, no crossing over occurs between the linked genes. All the linked genes will
pass into the same gamete, resulting in only parental gametes.

The following examples show complete linkage of genes in Drosophila.

Example 1
When pure-breeding Drosophila with long wings and grey body was crossed with pure-breeding
Drosophila with vestigial wings and ebony body, all the F1 offspring had long wings and grey body.

When the F1 offspring were mated, the F2 generation failed to give the 9:3:3:1 ratio. Instead about
75% of the F2 offspring had long wings and grey body, and the remaining 25% had vestigial wings and
ebony body. Note that these are parental phenotypes. Unlike the dihybrid cross studied earlier, there
were no recombinant phenotypes. Why is this so?

Genetic Interpretation

Let L represent the dominant allele for long wing,

l represent the recessive allele for vestigial wing.
G represent the dominant allele for grey body,
g represent the recessive allele for ebony body.

Parents long wing, grey body vestigial wing, ebony body

LG x lg
LG lg
Gametes
LG lg

F1 phenotype All long wing, grey body

F1 genotype
LG
lg

F1 cross long wing, grey body x long wing, grey body

LG LG
lg lg

Random fertilisation
Male gametes

LG lg

LG LG
LG
Female LG lg
gamete LG lg
lg
lg lg

F2 genotypic ratio 1 LG : 2 LG : 1 lg
LG lg lg

F2 phenotypic ratio 3 long wing, grey body : 1 vestigial wing, ebony body

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Example 2
When pure-breeding Drosophila with long wings and grey body was crossed with pure-breeding
Drosophila with vestigial wings and ebony body, all the F1 offspring had long wings and grey body.

When the F1 offspring were mated with pure-breeding Drosophila with vestigial wings and ebony body
in a test cross, it failed to give the 1:1:1:1 test cross ratio. Instead about 50% of the offspring had
long wings and grey body, and the remaining 50% had vestigial wings and ebony body. Note that
these are parental phenotypes. Unlike the dihybrid test cross studied earlier, there were no
recombinant phenotypes. Why is this so?

Genetic Interpretation

Let L represent the dominant allele for long wing,

l represent the recessive allele for vestigial wing.
G represent the dominant allele for grey body,
g represent the recessive allele for ebony body.

Parents long wing, grey body vestigial wing, ebony body

LG x lg
LG lg
Gametes
LG lg

F1 phenotype All long wing, grey body

F1 genotype
LG
lg

F1 test cross long wing, grey body vestigial wing, ebony body
LG x lg
lg lg

Random fertilisation
Male gametes

LG lg

Female LG lg
lg
gametes lg lg

Test cross genotypic ratio 1 LG : 1 lg

lg lg

Test cross phenotypic ratio 1 long wing, : 1 vestigial wing,

grey body ebony body

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Explanation for Examples 1 & 2

• If these two pairs of genes (L, l and G, g) are located on different (non-homologous) chromosomes,
according to Mendel’s Second Law of Independent Assortment, the F2 generation should consist of
four phenotypic groups at ratio 9:3:3:1 (for Example 1) and offspring generation should consist of
four phenotypic groups at ratio of 1:1:1:1 (for Example 2).

• The results of the 2 crosses did not show the expected dihybrid ratio (for Example 1) and
expected dihybrid testcross ratio (for Example 2).

• The two pairs of genes must be located very close together on the same chromosome and are
closely linked together.

• No crossing over occur between the 2 gene loci in the F1 flies and thus they are transmitted
together as a unit (as though they are one gene instead of two) as shown in Fig. 16 to produce
only two phenotypes with a monohybrid ratio 3:1 (in Example 1) and monohybrid test cross
ratio of 1:1 (in Example 2).

• The two phenotypes are both parental phenotypes (absence of recombinant phenotypes).

L L L
L
L
L
l
l
l
l l l

Fig. 18: Complete linkage (no crossing over) in F1 flies. Only two types of gametes ( LG and lg )are produced.

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 9.2 INCOMPLETE LINKAGE

Genes which are located some distance apart on the same chromosome generally show
incomplete linkage and thus can be separated when crossing over occurs during meiosis:
• Prophase I of meiosis: chiasmata may form between non-sister chromatids of homologous
chromosomes.
• At a chiasma, the non-sister chromatids break at corresponding points, exchange genetic material
and rejoin to form recombinant chromatids: crossing over.
• If the crossing over occurs between the 2 gene loci, there will be genetic recombination leading to
a new combination of alleles in gametes as shown in Fig. 19.
• Eventually, the separated chromatids end up in separate gametes, and after fertilisation, give rise
to new combinations of alleles in the offspring – such offspring are called recombinants.

L L L
L
L
L
l

l
l
l l
NCO l

L L
L
L
L
L
l

l
l
l l
l

CO

Fig. 19: Explanation of incomplete linkage in terms of chromosomes behaviour at meiosis (NCO = no crossing over
between the two genes, CO = crossing over).

As crossing over is a random process, offspring produced show a majority of parental allele
combinations and hence parental phenotypes and a minority of recombinant allele
combinations and hence recombinant phenotypes.

If we consider the same test cross in Example 2 again but this time assume incomplete linkage, we
get different results, as shown in Example 3.

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Example 3
When pure-breeding Drosophila with ebony body and vestigial wings were crossed with pure-breeding
Drosophila with grey body and long wings, all the F1 offspring showed grey body and long wings.
Sibling mating of F1 offspring failed to give a phenotypic ratio of 9:3:3:1 or 3:1 in the F2 generation.
Test cross on the F1 offspring yielded the following results:

Long wings, Vestigial wings, Long wings, Vestigial wings,

Phenotypes
Grey body Ebony body Ebony body Grey body
No. of offspring 184 176 16 24

With reference to the following data, draw a genetic diagram to explain the results of the test cross
between F1 offspring and pure-breeding Drosophila with vestigial wings and ebony body.

Genetic Interpretation

Let L represent the dominant allele for long wing,

l represent the recessive allele for vestigial wing.
G represent the dominant allele for grey body,
g represent the recessive allele for ebony body.

Parents long wing, grey body vestigial wing, ebony body

LG x lg
LG lg
Gametes
LG lg

F1 phenotype All long wing, grey body

F1 genotype
LG
lg

F1 test cross long wing, grey body vestigial wing, ebony body
LG x lg
lg lg
Random fertilisation
Male Gametes

LG lg Lg lG

Female LG lg Lg lG
lg
Gametes lg lg lg lg
Testcross Long Vestigial Long Vestigial
Phenotypes wings, wings, wings, wings,
grey body ebony body ebony body grey body
Observed no. 184 176 16 24
Parental Recombinants

Explanation
• The genes are incompletely linked, i.e. crossing over occurs between the linked genes.
• In a large sample of cells undergoing meiosis, crossing over (a rare event) will occur between the
two linked genes in only some of the cells, depending on how closely linked they are.
• Thus, 4 types of gametes are produced. Two of them are parental (larger proportion) and two
are recombinant (smaller proportion; only 2 of 4 chromatids cross over in some cells only).
• Percentage of recombinant gametes and thus recombinant offspring produced is comparatively
small.

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 9.3 DETECTION OF LINKAGE

A test cross between a double heterozygous individual with a double homozygous recessive
individual can be performed to detect if genes are unlinked, completely linked or incompletely linked.

If the genes are present on different chromosomes:

• 4 different phenotypes (gametes) are produced.
• Offspring should consist of four phenotypes with a ratio of 1:1:1:1.

If the genes are completely linked:

• Only 2 phenotypes (gametes) are produced.
• Offspring should consist of two parental phenotypes with a ratio of 1:1.
• There are no recombinant phenotypes.

If the genes are incompletely linked, i.e. crossing over occurs between the linked genes:
• 4 different phenotypes are produced.
• Two of them are parental and two are recombinant.
• Larger percentage of parental phenotypes and smaller percentage of recombinant phenotypes, i.e.
no fixed ratio.

Recall important points regarding linkage:

• Independent assortment only occurs when genes are located on different chromosomes.
• Genes located on the same chromosome do not assort independently and thus tend to be
inherited together i.e. linked.
• The linkage of linked genes can be either complete or incomplete. This depends on the relative
distance between each gene, as the probability of crossing over occurring between 2 gene
loci increases with increasing distance between the 2 gene loci.
• Phenotypic ratios of offspring from crosses involving linked genes (applies to both completely
and incompletely linked) deviate from the classic Mendelian ratios.
• Offspring with parental phenotypes occur at higher frequencies than those with recombinant
phenotypes.

Linked genes can be either in a coupling or repulsion arrangement. This is only applicable for
heterozygotes.

• Coupling:
Two dominant alleles are on one chromosome and the two recessives are on the homologous
partner.
AB
ab

• Repulsion:
Dominant allele is linked with a recessive on one chromosome.

Ab
aB

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 9.4 CHROMOSOME MAPPING

Thomas Hunt Morgan’s Chromosome Theory of Inheritance

Thomas Hunt Morgan was one of the first true geneticists. He and his "Fly
group" made tremendous contributions to our understanding of the role of
chromosomes and genes in inheritance.

Morgan had become interested in species variation, and in 1911, he established

the "Fly Room" at Columbia to determine how a species changed over time. For
the next 17 years, in a 16 x 23 ft. room, described by many as cramped, dusty,
smelly and cockroach ridden, Morgan and his students did ground-breaking
genetic research using Drosophila melanogaster, fruit flies.

Though initially against the idea that the behaviour of chromosomes can explain inheritance, Morgan
became the leading supporter of the idea. Morgan and his students (Alfred Sturtevant, Calvin Bridges,
Hermann Muller and others), developed the ideas, and provided the proof for the chromosomal
theory of heredity, genetic linkage, chromosomal crossing over and non-disjunction.

In 1933, Thomas Hunt Morgan received the Nobel Prize for Medicine for his work in establishing the
chromosomal theory of inheritance.

As genes are arranged in a linear order along the chromosome, the patterns of linkage have been
used to map chromosomes of a wide variety of organisms. This produces a linkage map which shows
the relative locations of genes along the chromosomes as shown in Fig. 20.

Fig. 20: Linkage map of a Drosophila Chromosome. Each homologous pair of chromosomes carries a pair of genes. The
alleles on a chromosomes form a linkage group because they tend to go together into a gamete. This simplified chromosome
map shows the relative positions of some of the genes on Drosophila chromosome 2. The distances between the genes
(number = map units) are equivalent to the percentage of crossing over events that occurs between various alleles.

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Chromosome mapping or construction of a linkage map for a particular chromosome is based on the
following principles:
• Crossing over can occur at any point along the chromosome.

• The chance of crossing over occurring between two linked genes on the chromosome is
proportional to the distance between them.

• If the two linked genes are far apart on a chromosome, the greater the statistical chance that
crossing over will separate them than if they were closer and therefore the greater the proportion
of recombinants that will be formed.

• The distance between genes can therefore be determined by the proportion of recombinants.

• For any particular pair of genes, the proportion of recombinants will always be about the same when
the testcross is repeated because the genes occupy fixed positions in the chromosomes and there
is a certain probability of a crossover occurring between them.

Therefore, the percentage of crossing over between the two linked genes can be taken as the
arbitrary units to represent the relative distance (not actual) between the genes concerned.

The percentage of crossing over is also known as the Crossover Value (COV) or the Recombination
Frequency (RF):

COV: Number of individuals showing recombination x 100%

Total number of offspring

Note: By convention a COV of 1% represents a relative distance of 1 centimorgan (cM) on the

chromosome.

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Order of Arrangement of Genes on a Chromosome

Crossing over not only enables us to find out the relative distance between linked genes on a
chromosome, but also their order of arrangement on the chromosome.

Suppose three genes A, B and C are linked on the same chromosome. In a breeding experiment,
the % recombination (COV) of characters controlled by these genes is found to be as follows:

Crossing over occurs between the genes COV (%)

A–B 9
B–C 5
A–C 4

• If the COV of A and B is 9%, they are 9 cM apart on the chromosome.

A B

• If the COV of B and C is 5%, they are 5 cM apart on the chromosome. But C may lie at the right of
B (Case 1) or at the left of B (Case 2).

Case 1
A B C

9 5

Case 2 4 5

A C B

Analysis:
The location is confirmed by checking the COV of A and C.
• Since the COV between A and C is 4%, order of arrangement of the genes is A – C – B (Case 2).
• Case 1 will only be correct if the COV between A and C is 14%.

The recombinant frequencies used to construct a linkage map for a particular chromosome are
obtained from experimental crosses. Therefore, making use of the COV of the various characters
obtained in numerous breeding experiments, we can prepare chromosome maps, showing the
locations of the various genes on the chromosomes.

This is illustrated in the subsequent three breeding experiments.

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Breeding Experiment 1
Crossing of pure-breeding grey body, normal eye colour flies with pure-breeding black body, purple
eye flies.

Parents grey body, normal eyes x black body, purple eyes

F1 All have grey body, normal eyes
F1 test cross grey body, normal eyes x black body, purple eyes
Offspring
Phenotypes No. of progeny
grey body, normal eyes 250
black body, purple eyes 234
black body, normal eyes 15
grey body, purple eyes 16
Total 515
15 + 16
COV = x 100% = 6.02%
515
The COV indicated that the genes for the body colour and eye colour were about 6 cM apart on one
of the autosomes.

Breeding Experiment 2
Crossing of pure-breeding grey body, long wings flies with pure-breeding black body, vestigial wings
flies.

Parents grey body, long wings x black body, vestigial wings

F1 All have grey body, long wings
F1 test-cross grey body, long wings x black body, vestigial wings
Offspring
Phenotypes No. of progeny
grey body, long wings 192
black body, vestigial wings 170
black body, long wings 43
grey body, vestigial wings 39
Total 444
43 + 39
COV = x 100% = 18.5%
444
The COV indicated that the genes for body colour and wing lengths were 18.5 cM apart on the same
autosome. From the results of the two breeding experiments, the linear order of the genes could be:

Case 1
6 cM 18.5 cM

black body purple eyes vestigial wings

OR
Case 2
6 cM 18.5 cM

purple eyes black body vestigial wings

If Case 1 is to be true, the COV for purple eyes and vestigial wings should be about:
18.5 – 6.0 = 12.5%
If Case 2 is to be true, the COV for purple eyes and vestigial wings should be about:

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 18.5 + 6.0 = 24.5%.

To find out which of the two orders is correct, a further experiment has to be carried out.

Breeding Experiment 3
Crossing of pure-breeding normal eyes, long wings flies with pure breeding purple eyes, vestigial
wings flies.

Parents normal eyes, long wings x purple eyes, vestigial wings

F1 All have normal eyes, long wings
F1 test-cross normal eyes, long wings x purple eyes, vestigial wings
F2
Phenotypes No. of progeny
Normal eyes, long wings 230
Purple eyes, vestigial wings 200
Purple eyes, long wings 32
Normal eyes, vestigial wings 28
Total 490

32 + 28
COV = x 100% = 12.2%
490

It is therefore evident that the linear order of the genes on the homologous autosomes is Case 1 as
shown below.

black body purple eyes vestigial wings

6 cM 12.2 cM

grey body normal eyes long wings

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 CONCEPT CHECK 2

In maize, coloured aleurone (R) is dominant to colorless (r). Yellow plant colour (y) is recessive to
ry
green (Y). Two plants, both heterozygous, were crossed to the double homozygous recessive , and
ry
gave the following progenies.

Phenotypes Progeny of plant 1 Progeny of plant 2

Coloured aleurone, green plant 88 23
Coloured aleurone, yellow plant 12 170
Colourless aleurone, green plant 8 190
Colourless aleurone, yellow plant 92 17
Total 200 400

From the data, calculate the percentage recombination between Y and R and discuss the linkage
between the genes in plant 1 and 2.

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 10. PHENOTYPIC VARIANCE

Phenotypic variance (VP) of a population has two components, genotypic variance (VG) and
environmental variance (VE):
VP = VG + VE

• VE is most easily determined when homozygous organisms are studied, i.e. VG = 0.

• VG is due to genotype, and includes the effects of additive genes, dominant genes and epistasis
(KIV: Inheritance Part II). The contributions of each to the phenotype can be estimated from
crosses involving homozygous varieties and their F1, F2 and backcross progeny.

10.1 EFFECT OF GENOTYPE ON PHENOTYPE

Variation in genotypes has a prominent effect on the phenotypic expression. There are various ways
of introducing genetic variation in a population. These include gene mutation, chromosomal mutation,
meiosis and sexual reproduction.

1. Gene Mutation
Gene mutation is defined as an inheritable change in the nucleotide sequence of DNA, which
occurs at a single gene locus on a chromosome, resulting in formation of new alleles. It can be
brought about by the following mechanisms:

• Deletion
This occurs when one or several nucleotides are removed from a sequence of nucleotides.
• Insertion
This occurs when one or several nucleotides are added to a sequence of nucleotides.
• Substitution
This occurs when a nucleotide is replaced by another.

Refer to Gene and Chromosomal Mutation notes for more information.

2. Chromosomal Mutation
Chromosomal mutation can be defined as:
• a change in the structure of a chromosome (involving several gene loci) or
• a change in the number of chromosomes.

Refer to Gene and Chromosomal Mutation notes for more information.

3. Meiosis And Sexual Reproduction

Meiosis (Recall Cell and Nuclear Division) generates genetic variation in the following ways:
• Crossing over of non-sister chromatids of homologous chromosomes during prophase I
results in new combinations of paternal and maternal alleles in each chromatids.
• Independent assortment of homologous chromosomes during metaphase I results in
random distribution of paternal and maternal chromosome in each gamete.

In sexual reproduction, the fusion of two haploid gametes (fertilisation) to form a diploid zygote
restores the diploid number. It also results in genetic variation due to random fusion of gametes
from each individual, as well as random mating between individuals in a population.

Important: All genetic variation arising from meiosis and sexual reproduction results in new
combination of existing alleles. It does not give rise to new alleles.

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 10.2 EFFECT OF ENVIRONMENT ON PHENOTYPE

The genotype of an organism is not always directly expressed in the phenotype. Gene expression
and the resultant phenotype are often modified through the interaction between an individual’s
particular genotype and the environment. Environmental factors which might affect gene expression
and the resultant phenotype include temperature, elevation, soil acidity and even diet.

1. Effect of Temperature
Example 1: Coat colour in Himalayan rabbits

A Himalayan rabbit has a white body with black ears, nose, feet and tail. If the fur on the back of the
rabbit is shaved and an ice-pack is fixed on the shaved region, left in position for weeks and kept cold,
new black fur instead of the original white fur) begins to grow below the ice-pack as shown in Fig. 21.

This is because all these Himalayan rabbits are homozygous for the ch allele of the tyrosinase gene,
which codes for a heat-sensitive form of the enzyme tyrosinase, which is needed for melanin
production resulting in black fur. Heat sensitive tyrosinase is active only when the air temperature
is below 33C.

Hence, only in parts of the body that are cool enough, e.g. extremities or underneath the ice-pack
does black fur grow.

Fig. 21: Coat colour of Himalayan rabbits is affected by temperature.

Example 2: Vestigial wings in Drosophila melanogaster

In Drosophila, vestigial wings are recessive to that of long wings.

The allele for vestigial wings is expressed at low temperatures. Drosophilas which are homozygous
recessive for vestigial wings will develop vestigial wings at 21C, intermediate wings at 26C and long
wings at 31C.

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2. Effect of Elevation
Apart from temperature, elevation also has an effect on the phenotypes of organisms. A classical
example is yarrow plants (Achillea millefolium). Genetically identical cuttings from yarrow plants
grown at three elevations grew differently at different altitudes.

Cuttings from one plant grew tall at the lowest and the highest elevation, but a third cutting remained
short at mid-elevation as shown in Fig. 22. Even though these plants were genetically identical, their
phenotypes differed in different environments.

Fig. 22: Effect of environment on yarrow plants. Yarrow plants grown at different elevation affects its growth.

3. Effect of Soil Acidity

Hydrangea, a common garden plant, may have different floral colours despite carrying the same
alleles as shown in Fig. 23. This colour variation is due to the differences in soil acidity in which the
plants grow, which affects the availability of aluminium to the plants.

In acidic soils (pH 5.5 or lower): Aluminum assumes a form that is easily absorbed by plant roots,
and thus flowers are predominately blue.

In soils where pH is 6.5 or higher: Aluminum is unavailable and flower color is pink. A single plant
can have both blue and pink flowers because of varying soil conditions around the plant.

Fig. 23: Effect of environment on Hydrangea flower colours where the same genetic variety range in color from blue-
violet to pink depending on the acidity of the soil .

4. Effect of Diet
HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance I 48
Example 1: Honey bees

A bee colony comprises three types of bees, mainly the queen, drones and workers. Drones are
males and are developed from unfertilized haploid eggs. On the other hand, the queen and the
workers are females and they develop from fertilised diploid eggs. Although the queen and
worker bees have the same amount of genetic material, they are phenotypically different. Not
only the worker bees are sterile, they are smaller and have larger mouthparts and modified legs as
compared to the queen bee.

The phenotypic differences between the queen and the worker bees are due to the diet of the bee
larvae (Fig. 24). After hatching, all the larvae are initially fed with royal jelly. Larvae destined to be
worker bees are switched to a diet containing honey and pollen. The larvae destined to be the queen
are fed with royal jelly. The high content of protein in royal jelly stimulates the formation and maturation
of the female reproductive system.

Fig. 24: Diet affects the diffentiation of honey bees.

Example 2: Late-onset diabetes in humans

This develops in genetically diabetic individuals who over-eat but not in genetically diabetic individuals
whose diet is low in sugars and lipids. The hormone insulin is secreted when blood glucose level
increases. Over-eating of sugary foods for a long period of time causes repeated stimulation of the
pancreas, which responds by secreting high levels of insulin.

However, repeated exposure of target cells to large amounts of insulin desensitises the cells’
responsiveness to insulin. This may result in the target cells failing to dispose of glucose in the usual
way, resulting in diabetes.

5. Effect of Light
Example 1: Freckling in humans
Several genes are responsible for freckling in humans but the extent of freckling is determined by
exposure to light.

Example 2: Chlorophyll synthesis in plants

The synthesis of chlorophyll in plants is genetically determined but light is also required.

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 INHERITANCE II

The chromosomal basis of inheritance sheds light in the pattern of transmitting genes from
parent to offspring.
When Gregor Mendel first started his investigations into inheritance, the concept of genes had not
existed yet. He used the term ‘traits’ in place of genes. By using genetic diagrams, the phenotypic and
genotypic ratios of filial generations can be predicted for crosses involving monohybrid or dihybrid
inheritance. In line with Mendelian genetics, pedigree diagrams can be used to predict the probability
of inheriting genetic diseases such as haemophilia and Huntington’s disease.
Non-Mendelian inheritance involves more complex traits. For example, some genes are found on sex
chromosomes while others involve multiple alleles. For example, alleles of some genes exhibit co-
dominance or incomplete dominance and some genes have multiple alleles or are found on the sex
chromosomes. Furthermore, phenotype may depend on interactions between two or more
genes, e.g. epistasis. In addition, the inheritance of linked genes does not follow Mendelian laws; in
predicting the phenotypic and genotypic ratios of filial generations for linked genes, the occurrence
and frequency of crossing over has to be considered.
This concept includes both Mendelian and non-Mendelian inheritance. Besides genetics, the
environment also plays a role in determining the phenotype of an organism. Statistical tests, such
as the chi-squared test, allow scientists to test the significance of differences between
observed and expected results of genetic crosses.
LEARNING OUTCOMES
Candidates should be able to:
Core Idea 2
(x) use genetic diagrams to solve problems in dihybrid crosses, including those involving
codominance, incomplete dominance, multiple alleles, sex linkage, autosomal linkage and
epistasis
(aa) describe the interaction between loci (epistasis) and predict phenotypic ratios in problems
involving epistasis (knowledge of the expected ratio for various types of epistasis is not
required; focus of this section is on problem solving)
(cc) explain the difference between genetic variation that is continuous (many, additive genes
control a characteristic) and genetic variation that is discontinuous (one or a few genes control a
characteristic)
(dd) use the chi-squared test to test the significance of differences between observed and expected
results
Use the knowledge gained in this section in new situations or to solve related problems.

LEARNING EXPERIENCES

• A random sampling of the length of rice grains or the height of classmates could be carried out.
Continuous variation, environmental influence, and the polygenic, additive role of many minor
genes can be credited as factors that contribute to the variation in length of rice grains or height of
classmates sampled.
• Carry out a chi-squared test by counting differently-coloured corn kernels on a cob. The
probability of the observed ratio departing significantly from the expected ratio using their
calculated chi-squared value can be used to establish the appropriate conclusion.

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 REFERENCES

1. Campbell and Reece: Biology, 10th edition

2. Klug et al: Concepts of Genetics, 9th edition
3. Pierce et al: Genetics – A Conceptual Approach
4. Snustad and Simmons: Principles of Genetics, 4th edition
5. Garvin: Skills in Advanced Biology Vol. 1: Dealing with Data
6. Brooker et al: Biology, International edition

WEBSITE RESOURCES

S/N QR Code What’s so interesting?

1.
Epistasis: Gene Interaction and Phenotype Effects (A closer look at epistasis
with a summary table)

2.
Gene Interactions (Non-epistatic and epistatic gene interactions explained in a
concise manner aided by pathways and diagrams)

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 2

 LECTURE OUTLINE

1. Introduction 5

2. Gene Interactions 5
2.1 Non-Epistatic Gene Interactions 6
2.2 Epistatic Gene Interactions 8
2.2.1 Recessive Epistasis 8

CONCEPT CHECK 1 10

2.2.2 Dominant Epistasis 12

2.2.3 Duplicate Recessive Epistasis 14
Table summary of modified F2 Mendelian dihybrid ratios 16
Schematic summary of the biochemical basis of modified F2 Mendelian 17
dihybrid ratios

CONCEPT CHECK 2 18

3. Variation 19
3.1 Discontinuous Variation 20
3.2 Continuous Variation 20
3.3 Causes of Genetic Variation in a population 21

4. Chi–squared (2) Test – A Type of Biostatistical Test 22

2 23
4.1 Step-by-step solution of Chi-squared ( ) Test Questions

CONCEPT CHECK 3 28

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 INHERITANCE

Mendelian Inheritance

Monohybrid Inheritance: one gene → one character

(e.g. gene C) (e.g. flower colour) Discrete phenotypic classes – no intermediates:
• Variation controlled by a single or a few gene(s)
Dihybrid Inheritance: two genes → two characters
(e.g. gene C and gene S) (e.g. flower colour and seed shape) • Little or no environmental effect on gene
expression
gene C → flower colour
• Phenotypic measurements represented on bar
gene S → seed shape
graphs
• Determine counts or ratios
Non-mendelian Inheritance • Statistical analysis: 2 test

Gene Interaction (GI): two or more genes → one character

(e.g. flower colour)

Substrate (Input) -----------------→ Intermediate -----------------→ Product (Output, i.e. flower colour pigment)
Enzyme A Enzyme B
 
Gene A Gene B

(I) Epistatic GI: Recessive Epistasis

Substrate (Input) -----------------→ Intermediate -----------------→ Product (Output, i.e. flower colour pigment)
Non-functional enzyme A Enzyme B
 
Gene A: genotype aa Gene B

(II) Epistatic GI: Dominant Epistasis

Substrate (Input) -----------------→ Intermediate -----------------→ Product (Output, i.e. flower colour pigment)
Enzyme A Enzyme B
Inhibitor I ----l  
 Gene A Gene B
Gene I: genotype I_

(III) Epistatic GI: Duplicate recessive Epistasis

Substrate (Input) -----------------→ Intermediate -----------------→ Product (Output, i.e. flower colour pigment)
Non-functional enzyme A Non-functional enzyme B
  Continuous Variation
Gene A: genotype aa Gene B: genotype bb Range of phenotypes – intermediates observed:
• Variation controlled by multiple additive genes
Gene A Gene B • Environmental factors influence degree of gene
  expression
Enzyme A Enzyme B • Phenotypic measurements represented on normal
distribution curves
Polygenic inheritance: two or more genes each
acting in an additive manner → one character • Determine population mean & standard deviation
flower colour pigment
(e.g. genes A, B, C and D) (e.g. flower colour) • Statistical analysis: t-test or standard error analysis

Enzyme C Enzyme D
 
Gene C Gene D

HWA CHONG INSTITUTION / 2021-2022 H2 BIOLOGY / Core Idea 2 / Inheritance II 4

 1. INTRODUCTION
In Inheritance Part I, we examined both the monohybrid and dihybrid inheritance. Monohybrid
inheritance involves the inheritance of a single character controlled by a single gene. While dihybrid
inheritance involves the inheritance of two characters, controlled by two different genes on two gene
loci. In the dihybrid inheritance cases we considered, the alleles segregated and assorted
independently, allowing us to predict the phenotypes of offspring from the genotypes of their
parents.
However, most characters are determined by the interaction of several genes. A single character
may be controlled by the interaction of two or more genes situated at different gene loci. In
Inheritance Part II, we will examine some of these interactions that result in a modification of the
classic Mendelian dihybrid ratio of 9:3:3:1.

2. GENE INTERACTIONS
The term "gene interaction" is often used to describe the idea that two or more genes influence
one particular character.

Commonly, the various gene products function in a metabolic pathway that contributes to
development of one particular phenotype as shown in Fig. 1:

Gene A: Gene B: Gene D:

Allele A encodes Allele B encodes Allele D encodes

functional enzyme A functional enzyme B functional enzyme D
amino acid intermediate intermediate
red pigment
tryptophan compound 1 compound 2
Allele a Allele b Allele d
(lack of enzyme A or (lack of enzyme B or (lack of enzyme D or
non-functional enzyme A) non-functional enzyme B) non-functional enzyme D)

vermillion pigment cinnabar pigment brown pigment

Fig. 1: Illustration of genes interacting together in a pathway. The four different eye pigments in Drosophila are
derived from the amino acid tryptophan in a metabolic pathway where genes A, B and D are involved. The final eye
pigmentation phenotype is influenced by the dominant allele present at all three gene loci.

The study of gene interactions reveals inheritance patterns that modify the classical Mendelian
dihybrid ratio (9:3:3:1). For instance, epistasis combines one or more of the four phenotypic
categories in various ways.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 5

 2.1 NON-EPISTATIC GENE INTERACTIONS

Two independently assorting genes (i.e. unlinked) may interact to influence a single character.

Some of the first evidence of a character being influenced by more than one gene was obtained
from breeding experiments with chickens.

Although the basic ratio is the same as in dihybrid inheritance involving unlinked genes, the gene
interaction case cited below and dihybrid inheritance are essentially different:
• dihybrid inheritance studies two characteristics (e.g. comb shape and feather colour)
controlled by two genes (essentially one gene → one characteristic relationship).
• gene interaction studies one characteristic controlled by two or more genes (essentially
many genes → one characteristic relationship).

Worked Example 1: Comb Shape in Chicken

Chicken comb shape is determined by interactions between 2 gene loci. Looking at one gene locus
at a time:

P gene locus: provided that the dominant rose comb (R) allele is absent:
dominant pea comb allele (P) results in a pea-shaped comb, i.e. PPrr or Pprr
recessive pea comb allele (p) results in a single comb, i.e. pprr

R gene locus: provided that the dominant pea comb (P) allele is absent:
dominant rose comb allele (R) results in a rose comb, i.e. ppRR or ppRr
recessive rose comb allele (r) results in a single comb, i.e. pprr

When both dominant alleles are present, as in PPRR, PpRR, PPRr and PpRr genotypes, a walnut
comb is observed.

Show the result of a cross between a pure-breeding rose comb cock and a pure-breeding pea comb
hen and that between the F1 offspring.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 6

Let:
P represent the dominant allele for presence of pea comb
p represent the recessive allele for absence of pea comb
R represent the dominant allele for presence of rose comb
r represent the recessive allele for absence of rose comb

Explanation
Parental • The shape of the chicken
Rose comb ♂ Pea comb ♀
phenotypes comb is determined by two
Parental independently assorting
ppRR  PPrr genes, P and R, each with
genotypes
two alleles, P/p and R/r,
Parental pR Pr respectively.
gametes
• The F1 hybrids between a
F1 genotype all PpRr pure-breeding rose-comb cock
(ppRR) and a pure-breeding
pea-comb hen (PPrr) are of
F1 phenotype all walnut comb double heterozygous
genotype (PpRr) – they will
F1 phenotype Walnut comb ♂ Walnut comb ♀ have the walnut comb
phenotype.

F1 genotype PpRr  PpRr • If these F1 hybrids are crossed

with each other, all four types
PR Pr pR pr PR Pr pR pr of combs will appear in the F2
F1 gametes progeny as shown in Fig. 2.

F1 male gametes
Random
fertilisation PR Pr pR pr

PR PPRR PPRr PpRR PpRr

Pr PPRr PPrr PpRr Pprr

F1 female
gametes pR PpRR PpRr ppRR ppRr

pr PpRr Pprr ppRr pprr

F2 genotypic ratio 9 P_R_ : 3 P_rr : 3 ppR_ : 1 pprr

F2 phenotypic ratio 9 walnut comb : 3 pea comb : 3 rose comb : 1 single comb

Fig. 2: Comb shape in chickens of different breeds. From left to right: walnut (hybrid from cross between chickens with
rose and pea combs), pea (Brahmas), rose (Wyandottes) and single (Leghorns). Possible genotypes resulting in
development of respective combs are shown in the table above.

Biochemical basis of comb shape in chickens

Different combinations of alleles from the two genes result in different phenotypes of a single
character, presumably due to the interaction of their gene products, each of which contributes to
the comb shape at the biochemical or cellular level.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 7

 2.2 EPISTATIC GENE INTERACTIONS

Epistasis (Greek for "stoppage") is inferred when the expression of an allele of one gene
suppress / inhibit the expression of alleles of a different gene.

When two or more genes influence one characteristic, an allele at one gene locus may have an
overriding effect on the genotype at a different locus.
• Result: different phenotypic expression
• Epistasis is different from complete dominance, i.e. complete dominance entails the masking of
alleles at the same gene locus.

An epistatic gene is one which is able to suppress / inhibit the effect of a gene at a different
locus. The epistatic gene can be (i) recessive or (ii) dominant in their effects.

The suppressed gene is termed the hypostatic gene.

The mode of epistasis (i.e. recessive or dominant) is often revealed by certain phenotypic ratios in
the F2 generation.

2.2.1 RECESSIVE EPISTASIS

For recessive epistasis, two recessive alleles at the epistatic gene locus will suppress / inhibit
the effect of either allele of the hypostatic gene at a different locus.

Worked Example 2: Coat Colour in Labrador Retrievers

Recessive epistasis is seen in the genes that determine coat colour in Labrador retrievers, which
may be black, brown, or yellow; their different coat colours are determined by interactions between
genes at two loci.

Gene locus Dominant Recessive

E: Pigment E allele allows deposition of dark e allele prevents deposition of dark pigment,
deposition pigment (black or brown) causing the hair to be yellow. e is hence a
recessive epistatic allele to alleles B and b at a
different gene locus.
B: Pigment B allele codes for black pigment b allele codes for brown pigment
colouration

A cross of true-breeding black (EEBB) and yellow (eebb) dogs produces all black dogs (EeBb). A
cross between the F1 dogs produces a genetic ratio of 9 black : 3 brown : 4 yellow dogs in the F2
generation.

Explain, with a genetic diagram, why the F2 phenotypes do not follow the classical Mendelian
dihybrid ratio of 9:3:3:1.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 8

Let:
E represent the dominant allele for deposition of pigment
e represent the recessive allele for no deposition of pigment OR preventing deposition of pigment
B represent the dominant allele for black pigment
b represent the recessive allele for brown pigment

Explanation
Parental • Yellow dogs can carry alleles B
Black coat ♂ Yellow coat ♀ or b, for either black or brown
phenotypes
pigment deposition
Parental respectively, but these alleles
EEBB  eebb
genotypes are not expressed in their coat
colour.
Parental EB eb
gametes • Genotype ee is epistatic to B
and b, because ee suppresses
F1 genotype all EeBb the expression of the alleles for
black and brown pigments in the
phenotype.
F1 phenotype all black coat
• Alleles B and b are hypostatic
to e as their expression is
F1 phenotype Black coat ♂ Black coat ♀ suppressed by the presence of 2
copies of e.
F1 genotype EeBb  EeBb • In this case, e is a recessive
epistatic allele because: two
copies of the recessive allele
ee must be present to
EB Eb eB eb EB Eb eB eb suppress the expression of the
F1 gametes
alleles encoding the black and
brown pigments at the second
locus as shown in Fig. 3.

F1 male gametes
Random fertilisation
EB Eb eB eb

EB EEBB EEBb EeBB EeBb

Eb EEBb EEbb EeBb Eebb

F1 female
gametes eB EeBB EeBb eeBB eeBb

eb EeBb Eebb eeBb eebb

F2 genotypic ratio 9 E_B_ : 3 E_bb : 4 (3 eeB_ + 1 eebb)

F2 phenotypic ratio 9 black coat : 3 brown coat : 4 yellow coat

Colour of pigment Black Brown Black , Brown

Pigment deposition + + - -
Fig. 3: Effect of epistatic interactions on coat colour in dogs. The coat colour seen in Labrador retrievers is an
example of the interaction of two genes, each with two alleles. The E gene determines if the pigment will be deposited in
the fur, and the B gene determines the colour of the pigment deposited.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 9

Biochemical basis of coat colour in Labrador retrievers (shown in Fig. 4)

Gene B Gene E
Allele B Allele E

Enzyme B Deposition of pigment Colouration

Brown Black (brown or black)
T
ee suppresses the
deposition of pigment,
hence dog is yellow.

Fig. 4: Illustration of the interaction between two genes that control the characteristic of coat colour in Labrador
Retrievers. Dogs with genotype B_ encode a functional form of enzyme B. The genotype E_ encodes a functional form of
enzyme E, allowing the deposition of pigment (brown or black). The presence of the genotype ee (i.e. non-functional
enzyme E) prevents any deposition of pigment and the dog will be yellow.

Recessive epistasis shows 9: 3: 4 phenotypic ratio with a double heterozygous cross.

CONCEPT CHECK 1

In mice, epistasis is observed when the homozygous recessive bb genotype occurs at a specific
locus. bb genotype suppresses pigment synthesis, which is controlled by another gene locus with
alleles A and a. Mice with bb genotype are albino regardless of genotype at the A locus, mice with
aa genotype and at least one dominant B allele are black and mice with at least one dominant
allele at each locus are agouti. This results in a pattern of pigmentation whereby each strand of hair
has a yellow band. The agouti mice have an overall grey phenotype as shown in Fig. 5 and 6.

Fig. 5: Agouti mice and pattern of pigmentation

The probable pathway is represented below:

Allele A
Allele B

Deposition of yellow pigment

Enzyme B
Precursor Intermediate Product
(white fur) (coloured fur: black) (coloured fur: agouti)
T
bb inhibits the conversion of white to black
pigment, hence mouse is white / albino.
Fig. 6: Illustration of the interaction between two genes that control the characteristic of coat colour in mice.
Mouse with the genotype B_ encode a functional form of enzyme B. The genotype A_ encodes a functional form of
enzyme A allowing the deposition of yellow pigment. The presence of genotype aa prevents any deposition of pigment
and the mouse will be white.

A range of modified offspring phenotypic ratios can be obtained depending on the genotypes of the
parents. Can you predict the offspring phenotypic ratios with the following sets of parents?

Parental phenotype(s) Parental genotype(s) Phenotypic ratio

1) agouti x agouti BbAa x BbAa
2) agouti x black BbAa x Bbaa
HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 10
Let:
B represent the dominant allele for pigment synthesis / black fur
b represent the recessive allele for no pigment synthesis / albino fur
A represent the dominant allele for yellow pigment deposition / agouti fur
a represent the recessive allele for no yellow pigment deposition, i.e. black fur

1) Agouti  Agouti

Parental phenotypes Agouti ♂ Agouti ♀

Parental genotypes BbAa  BbAa

Parental gametes BA Ba bA ba BA Ba bA ba

Male gametes
Random fertilisation
BA Ba bA ba

BA

Ba
Female
gametes bA

ba

Offspring genotypic ratio

Offspring phenotypic ratio

2) Agouti  Black

Parental phenotypes Agouti ♂ Black ♀

Parental genotypes BbAa  Bbaa

Parental gametes BA Ba bA ba Ba ba

Male gametes
Random fertilisation
BA Ba bA ba

Ba
Female
gametes ba

Offspring genotypic ratio

Offspring phenotypic ratio

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 11

 2.2.2 DOMINANT EPISTASIS

For dominant epistasis, one dominant allele at the epistatic gene locus will suppress / inhibit
the effect of both alleles of the hypostatic gene at a different locus.

Worked Example 3: Fruit Colour in Summer Squash

Dominant epistasis is seen in the interaction of two gene loci that determine fruit colour in summer
squash, which is commonly found in one of three colours: yellow, white, or green.

Gene locus Dominant Recessive

W: Inhibition of pigment Allele W: Allele w allows pigment
production • codes for an inhibitor for pigment production. production
• is a dominant epistatic allele to alleles Y
and y at a different gene locus - one copy is
sufficient to suppress / inhibit the
expression of the pigment-producing alleles.
Y: Pigment production Allele Y codes for yellow pigment production Allele y codes for green
pigment production

Let:
W represent the dominant allele for inhibition of pigment production
w represent the recessive allele for pigment production
Y represent the dominant allele for yellow pigment production
y represent the recessive allele for green pigment production
Explanation
Parental • 12/16 or 3/4 of the plants produce
White ♂ Green ♀ white squash.
phenotypes
• 3/16 + 1/16 = 4/16 = 1/4 of the
Parental
WWYY  wwyy plants produce coloured squash.
genotypes
• This suggests that a dominant
Parental WY wy allele (W) at one locus encodes
gametes an inhibitor for the production of
pigment (YY, Yy, yy), resulting in
F1 genotype all WwYy white progeny.
• Among the F2 plants with
F1 phenotype all white pigmented fruit, the ratio of yellow
to green fruit is 3:1.
• The coloured squash hence
F1 phenotype White ♂ White ♀
shows monohybrid 3:1 ratio
produced by a cross between two
F1 genotype WwYy  WwYy heterozygous individuals.
• The second locus determines the
F1 gametes WY Wy wY wy WY Wy wY wy type of pigment produced in the
squash, with yellow (Y_) dominant
over green (yy).
F1 male gametes
Random fertilisation
WY Wy wY wy

WY WWYY WWYy WwYY WwYy

F1 female Wy WWYy WWyy WwYy Wwyy

gametes wY WwYY WwYy wwYY wwYy
wy WwYy Wwyy wwYy wwyy
F2 genotypic ratio 12 (9 W_Y_ + 3 W_yy) : 3 wwY_ : 1 wwyy
F2 phenotypic ratio 12 white : 3 yellow : 1 green

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 12

Biochemical basis of fruit colour in Summer squash (shown in Fig. 7)

Gene W Gene Y
Allele W inhibits the conversion
of white to green pigment Allele Y

┴
E1 E2
White Green Yellow

Fig. 7: Illustration of the interaction between two genes that control the characteristic of fruit colour in Summer
squash. A colourless (white) precursor is converted by enzyme E1 (meaning: ww, the inhibitor W for the enzyme is non-
functional) into green intermediate, which is then converted into yellow pigment (product) in the fruit by enzyme E2 (Y_).
Plants with genotype yy do not encode a functional form of E2.

Inhibition of Ability to
Presence / Presence / Presence /
conversion of convert
Genotype absence of absence of absence of Phenotype
precursor to intermediate
precursor intermediate product
intermediate to product
wwY_ + No + Yes + Yellow
wwyy + No + No - Green
W_Y_ + Yes - Yes - White
W_yy + Yes - No - White

Dominant epistasis shows 12: 3: 1 phenotypic ratio with a double heterozygous cross.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 13

 2.2.3 DUPLICATE RECESSIVE EPISTASIS

For duplicate recessive epistasis, two recessive alleles at either of the two gene loci will
suppress / inhibit the effect of the dominant allele at the other locus.

Worked Example 4: Flower Colour In Sweet Peas

Sweet pea flowers (Lathyrus odoratus) are either purple (containing anthocyanin pigment) or
white (without pigment). A cross between two white flowers produced F1 heterozygotes which all
had purple flowers. When the F1 heterozygotes were crossed, a ratio of 9 purple flowers: 7 white
flowers were obtained in the F2 generation.
Each dominant allele encodes an enzyme that controls a step in the synthesis of anthocyanin from
a biochemical precursor. If a dominant allele is absent, its step in the biosynthetic pathway is
blocked and anthocyanin will not be produced as shown in Fig. 8.

Gene C Gene P

Allele C Allele P

E1 E2 Product
Precursor Intermediate
(Purple anthocyanin)
(Colourless) (Colourless)

Fig. 8: Effect of epistatic interactions on flower colour in sweet peas. The flower colour seen in sweet peas is an
example of the interaction of two genes, each with two alleles. Both dominant alleles (C and P) must be present for the
synthesis of the anthocyanin pigment in sweet pea flowers.

Genotype Presence / absence Presence / absence of Presence / absence of Phenotype

of precursor intermediate anthocyanin
C_P_ + + + Purple
ccP_ + - - White
C_pp + + - White
ccpp + - - White

Duplicate recessive epistasis shows 9: 7 phenotypic ratio with a double heterozygous cross.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 14

Let:
C represent the dominant allele for production of the intermediate pigment
c represent the recessive allele for no production of the intermediate pigment
P represent the dominant allele for production of anthocyanin
p represent the recessive allele for no production of anthocyanin

Explanation
Parental • There are two independently
White ♂ White ♀ assorting gene loci, C and P,
phenotypes
involved in anthocyanin
Parental
CCpp  ccPP synthesis. The gene at each
genotypes locus has a recessive allele that
Parental Cp cP
abolishes pigment production.
gametes • F1 offspring are all CcPp double
heterozygotes with purple
F1 genotype all CcPp
flowers.

F1 phenotype all purple • A dominant allele at each gene

locus (i.e. C_P_) is necessary
for the synthesis of anthocyanin.
F1 phenotype Purple ♂ Purple ♀
• In the F2 generation, 9/16 of the
plants are C_P_ and have purple
F1 genotype CcPp  CcPp flowers while the remaining 7/16
are homozygous for at least one
F1 gametes CP Cp cP cp CP Cp cP cp of the recessive alleles and have
white flowers.
• The double recessive
homozygotes, ccpp, are not
phenotypically different from the
either of the single recessive
homozygotes, C_pp and ccP_.
• Each of the recessive alleles is
epistatic over the dominant allele
of the other gene.
• cc is epistatic to the P locus
because cc prevents the
phenotypic expression of the
alleles at the P locus. Similarly,
pp is epistatic to the C locus.
• This type of interaction is termed
duplicate recessive epistasis.
F1 male gametes
Random fertilisation
CP Cp cP cp

CP CCPP CCPp CcPP CcPp

Cp CCPp CCpp CcPp Ccpp

F1 female
gametes cP CcPP CcPp ccPP ccPp

cp CcPp Ccpp ccPp ccpp

F2 genotypic ratio 9 C_P : 7 (3 C_pp +3 ccP_+ 1 ccpp)

F2 phenotypic ratio 9 purple : 7 white

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 15

 SUMMARY OF MODIFIED F2 MENDELIAN DIHYDRID RATIOS

TABLE SUMMARY OF THE MODIFIED F2 MENDELIAN DIHYBRID RATIOS PRODUCED BY

VARIOUS TYPES OF GENE INTERACTION

(Gene A and gene B are two independently assorting gene loci, gene A is epistatic over gene B)

Phenotypic Genotype
Type of interaction Example
ratio A_B_ A_bb aaB_ aabb
Comb shape in
9:3:3:1 9 3 3 1 Non-epistatic
chicken
Recessive epistasis in a
double heterozygous cross. Coat colour in
(aa epistatic to B and b) Labrador
9:3:4 9 3 4
retrievers and
aa encodes non-functional mice
gene product
Dominant epistasis in a double
heterozygous cross.
(A epistatic to B and b)
Colour in
12:3:1 12 3 1
summer squash
A encodes functional gene
product that acts as an
inhibitor
Duplicate recessive epistasis
in a double heterozygous
cross.
(aa epistatic to B and b;
bb epistatic to A and a)
Flower colour in
9:7 9 7
sweet pea
aa encodes non-functional
gene product

bb encodes non-functional
gene product
Other ratios not covered in lecture (potentially new scenarios)
-
9:6:1 9 6 1 Duplicate interaction
Duplicate dominant epistasis
in a double heterozygous
cross.
15:1 15 1 -
(A epistatic to B and b;
B epistatic to A and a)

Dominant and recessive

epistasis in a double
13:3 13 3 heterozygous cross. -
(includes aabb)
(A epistatic to B and b;
b epistatic to A and a)

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 16

 SCHEMATIC SUMMARY OF THE BIOCHEMICAL BASIS OF THE
MODIFIED F2 MENDELIAN DIHYBRID RATIOS
Type of Biochemical basis
F2
inheritance /
Phenotypic
Gene KEY: E = Enzyme (Gene product),
ratio
interaction
A_

Dihybrid E1
inheritance A (colourless) colour
(two unlinked 9:3:3:1 B shape
genes) E2

B_

Non-epistatic (e.g. comb shape in poultry)

R_pp
Non-epistatic
Rose R_P_
gene
9:3:3:1 Single
interaction Walnut
Pea
rrP_

9:3:4 Recessive epistasis (ee epistatic to B and b)

E.g. coat colour of Labrador retriever
E_
B_
eebb→yellow
eeB_→yellow Deposition of
E_bb→brown Brown Enzyme B Black pigment Colouration
E_B_→black (brown or
T
ee inhibits the black)
deposition of pigment,
hence dog is yellow.
12:3:1 Dominant epistasis (W epistatic to Y and y)
Epistatic E.g. fruit colour of summer squash
gene
interactions W_ Y_
W_yy→white
W_Y_→white
wwY_→yellow ┴
E
┴
1
Intermediate E2
wwyy→green Precursor Yellow
(White) (Green)

9:7 Duplicate recessive epistasis

(cc epistatic to P and p; pp epistatic to C and c)
E.g. flower colour of sweet pea

C_P_→Purple
Precursor E1 Intermediate E2
C_pp→white Purple
ccP_→white (colourless) product
pigment
ccpp→white (colourless)
C_ P_

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 17

 CONCEPT CHECK 2

Pure-breeding cats with brown coats were mated with pure-breeding cats with white coat. All the
resulting F1 offspring were white. When pairs of these F1 were allowed to interbreed they produced
the resulting F2 ratio – 118 white coat : 32 black coat : 10 brown coat. Draw a genetic diagram to
explain both these crosses.

Let:
W represent the dominant allele that inhibits pigment production
w represent the recessive allele for pigment production
B represent the dominant allele for black fur
b represent the recessive allele for brown fur

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 18

 3. VARIATION

"Variation" describes the recognisable differences in characteristics (e.g. height, weight, skin
colour) between organisms of the same natural population or species.

In any large population, two forms of variations occur: discontinuous and continuous.

Studies of variation in a certain character involve measuring the expression of that characteristic
in a large number of organisms within the population.

Results are plotted as a bar chart or histogram showing the frequency distribution of the different
traits of that character.

3.1 DISCONTINUOUS VARIATION 3.2 CONTINUOUS VARIATION

Variation in characters of type Variation in characters of degree
Observable 1. Phenotypes are definite and clear 1. Phenotypes not clear cut and cannot be
phenotype cut. They can be divided into divided into distinct contrasting groups –
distinct groups – discrete range of phenotypes observed.
phenotypic classes observed.
• Intermediates are not • Intermediates are observed
observed
No. of genes 2. Variation controlled by a single or 2. Variations controlled by the combined
controlling a few gene(s). This gene may effect of multiple additive genes and
phenotypic have two or more alleles. are thus known as polygenic
variation inheritance.
Genes act on phenotype in an additive
manner. Effects of single genes are too
slight to be detected.
The combined effect of these genes can
produce individuals of infinite phenotypic
varieties.

Effect of 3. There is little or no environmental 3. Phenotypes can be modified by the

environment effect on the phenotypic cumulative effect of varying
on phenotype expression of the gene(s). environmental factors acting on the
different genotype.
E.g. in human: ABO blood group.
Although the genotype of an organism is
determined at the time of fertilisation, the
degree of expression allowed to this
genetic potential hinges on
environmental factors during the
development of the organism (see point
6, human intelligence)

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 3.1 DISCONTINUOUS VARIATION 3.2 CONTINUOUS VARIATION
4. Phenotypic measurements are normally 4. Phenotypic measurements form a normal
represented on bar graphs. distribution curve that has a continuous
range of intermediate forms between two
extremes. These are normally represented on
histograms.
Mode of phenotypic measurement

It is impossible to obtain a normal distribution Most organisms in the population fall in the middle
curve for such variation because the of the range with approximately equal numbers
phenotypic classes are distinct. showing the extreme forms of the characteristic.

5. Qualitative: analysed by making counts 5. Quantitative: statistical analyses give

and ratios. estimates of population parameters such as
the mean and standard deviation.
6. E.g. Inheritance of height in peas 6. E.g. Height, weight and intelligence in humans

P 1) As the
Dwarf x Tall number of
Number tt TT gene loci
of plants affecting the
characteristic
increases,

Height

F1 Tt
Tall selfed
Number
Examples

of plants

Height

2) the number
F2
of phenotypic
Tall ¾ classes
Number
increases.
of plants
Dwarf ¼ The results of crossing individuals heterozygous for
different numbers of gene pairs or gene loci affecting a
characteristic. The genetic ratios (on the X-axis) resulting
from crossing two heterozygotes when polygenic
Height inheritance is in operation with 1-5 gene pairs. The
histogram bars indicate the distinct F2 phenotypic classes,
ranging from one extreme (left end) to the other extreme
(right end). Each phenotype results from a different number
of additive alleles.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 20

 3.3 CAUSES OF GENETIC VARIATION IN A POPULATION

In asexually reproducing organisms:

DNA replication is so highly accurate and almost error-free that there is little possibility of
variation in the genotype. Any apparent variation between asexually reproducing organisms is
almost always the result of environmental influences.

In sexually reproducing organisms:

Ample opportunities for genetic variation arise via:

1. Crossing-over between non-sister chromatids of homologous chromosomes during

prophase I of meiosis.
2. Independent assortment of bivalents at the metaphase plate during metaphase I of
meiosis.
3. Random fertilisation

The above three sources arising from meiosis and sexual reproduction accounts for new
combination of alleles, which is the basis of continuous variation.

However, these sources of variation do not generate new alleles that are necessary to give rise to
new species (KIV: Biological Evolution). Such changes are ultimately caused by mutations.

4. A mutation is a change in the structure of a gene i.e. nucleotide sequence (gene mutation)
or in the structure or number of chromosomes (chromosomal mutation). Most mutations
occur in somatic cells, i.e. somatic mutations, and are not passed from one generation to the
next.

Only mutations occurring during the formation of gametes (i.e. germline mutations) can
be inherited. These mutations produce distinct differences between individuals, and
frequently form the basis of discontinuous variation.

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 4. CHI-SQUARED (2) TEST – A TYPE OF BIOSTATISTICAL TEST

A genetic diagram, whether of monohybrid or dihybrid inheritance, is only a prediction of the likely
outcome in the offspring generation. It shows the probable results with the following assumptions:
• Fertilisation is random.
• There is equal opportunity of survival among offspring.
• A large number of offspring are produced (i.e. large sample size).

For example, in monohybrid inheritance, Mendel's idea was that segregation of alleles during
meiosis accounts for the 3:1 ratio in the F2 generation. The data from his monohybrid crosses fit
very closely to the expected ratio of 3:1 as shown in Fig. 10.

F2 Generation
Character F1 Generation
Dominant Form Recessive Form Phenotypic Ratio
Stem height
All tall 787 tall 277 dwarf 2.84 : 1
Tall x Dwarf
Flower colour
All purple 705 purple 224 white 3.15 : 1
Purple x White
Pod colour
All green 428 green 152 yellow 2.82 : 1
Green x Yellow
Seed shape
All round 5474 round 1850 wrinkled 2.96 : 1
Round x Wrinkled

Fig. 10: Mendel’s experimental results. This table illustrates four of the seven characters Mendel studied in his
crosses of the garden pea and presents the data he obtained from these crosses. Each pair of traits appeared in the F 2
generation in a ratio very close to 3:1.

However, there is a chance that pollen grains of one genetic makeup may be more likely to fuse
with egg cells than another. Or if the cross produces very few progeny, the progeny may not
appear in the expected proportions.

This would result in a situation where the observed outcome cannot be clearly attributed to the
probabilities described by genetics alone. To test this, a chi-squared (2) test is required.

What is the chi-squared (2) test?

• The chi-squared (2) test is a statistical test for the significance of data that consists of
discontinuous / discrete variables.

• Statistical tests are done to see how well the observed experimental results fit the expected
results, i.e. ‘the goodness of fit’ between the observed and expected results.

• When observed ratios of phenotypic classes deviate from expected ratios, there is a need to test
whether this deviation or difference is due to CHANCE (meaning: the expected ratio has been
correctly predicted) or due to an incorrect prediction of expected ratios.
O The larger the difference between observed and expected results, the more likely that the
hypothesis is incorrect and hence, is not due to chance alone.
O The smaller the difference between observed and expected results, the more likely that the
hypothesis is correct, and hence is due to chance alone.

• The calculated 2 value is compared against a chi-squared distribution table to assess if the
difference between observed and expected results is statistically significant.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 22

 4.1 STEP-BY-STEP SOLUTION OF CHI-SQUARED (2) TEST QUESTIONS

1. State the hypotheses.

H0: There is no difference from the expected …… ratio

HA: There is difference from the expected …… ratio

• The NULL HYPOTHESIS (H0) states that there is no significant difference between the
observed and expected results. It assumes that any differences are due to chance.

• The ALTERNATIVE HYPOTHESIS (HA), states that there is significant difference

between the observed and expected results. It assumes that differences are not due to
chance.

E.g. Using Mendel’s data on monohybrid inheritance for stem height in pea plants,

H0: There is no difference from the expected 3 : 1 F2 phenotypic ratio

HA: There is difference from the expected 3 : 1 F2 phenotypic ratio

2. Calculate the expected number of individuals for each phenotypic class.

The expected values for each phenotypic class are obtained by calculating the proportion of
the total number of offspring that are expected to fall within that phenotypic class.

E.g. Using Mendel’s data on monohybrid inheritance for stem height in pea plants,

¾ of the total number of offspring are expected to display the dominant phenotype, i.e. tall stem,
¼ of the total number of offspring are expected to display the recessive phenotype, i.e. dwarf
stem.

3. Calculate the 2 value.

The calculated chi-squared value (2calc) is obtained by using the following formula:

d2 (O − E )2
 2 calc =  E
=  E

where  is sum of
d is the difference between observed (O) and expected (E) results (i.e. the deviation)

E.g. Using Mendel’s data on monohybrid inheritance for stem height in pea plants,

(O - E)2
Phenotype O E d=O-E (O - E)2
E
Tall stem 787 3/4 x 1064 = 798 787 – 798 = -11 121 0.1516

Dwarf stem 277 1/4 x 1064 = 266 277 – 266 = 11 121 0.4549

Total 1064 1064  = 0.6065

➔ 2calc = 0.61

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 23

4. Compare the 2calc value against a 2 probability table.

An abstracted version of the probability 2 probability table is shown below.

Probability (p)
Degrees of In a 2 probability table:
freedom 0.9 0.5 0.1 0.05 * 0.01 **
1 0.02 0.46 2.71 3.84 6.63 • The row to be read is
determined by the
2 0.21 1.39 4.61 5.99 9.21
degree of freedom.
3 0.58 2.37 6.25 7.81 11.34
4 1.06 3.86 7.78 9.49 13.28
• The column to be read
5 1.61 4.35 9.24 11.07 15.09
is determined by the
6 2.20 5.35 10.64 12.59 16.81 level of significance.
7 2.83 6.35 12.02 14.07 18.48
8 3.49 7.34 13.36 15.51 20.09
*Probability of 0.05 - statistically significant level **Probability of 0.01 – highly significant level

(a) Degree of freedom (df)

Calculate the number of degrees of freedom using the following formula:

df = n – 1 where n is the number of phenotypic classes

First, determine how many phenotypic classes there are in the investigation being carried out. If
there are 2 phenotypic classes, the degree of freedom (df) is 1.

• The degree of freedom measures the number of classes of data (in this case, phenotypic classes) that
are independent of each other. The degree of freedom measures the spread of the data and is always
one less than the number of classes of data.

• In the case of 2 phenotypic classes where the total number of offspring is known, when the number in
any one phenotypic class has been determined, the number in the second class is fixed. Hence, one is
subtracted from the number of phenotypic classes.

(b) Level of significance (α)

State the level of significance:

• There are two critical theoretical values (cut-off points) of  = 0.05 and  = 0.01, against
which 2calc is usually compared to decide whether or not to reject the null hypothesis.

• For Biology, unless stated otherwise, we take the level of significance to be 0.05.

(c) Critical chi-squared value (2crit)

From the 2 probability table, obtain the critical theoretical 2 value (2crit), stating it as
2crit, df = __, =0.05 = __________.

E.g. Using Mendel’s data on monohybrid inheritance for stem height in pea plants,
2crit, df = 1, =0.05 = 3.84

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 24

5. Write a conclusion.

If 2calc > 2crit ,

• the probability that chance alone is the reason for the difference between observed and
expected results / ratio is less than 5%.
• The deviation is significant.
• Hence, reject H0 in favour of HA.

OR

If 2calc < 2crit,

• the probability that chance alone is the reason for the difference between observed and
expected results / ratio is more than 5%.
• The deviation is not significant.
• Hence, do not reject H0.

E.g. Using Mendel’s data on monohybrid inheritance for stem height in pea plants,

Since 2calc (= 0.61) < 2crit (=3.84),

the probability that chance alone is the reason for the difference between observed and
expected 3 : 1 F2 phenotypic ratio is more than 5%.

The deviation is not significant.

Hence, do not reject H0.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 25

Worked Example 5: Wing Length in Drosophila Spp.

In Drosophila, normal wings are dominant to vestigial wings. Two normal winged individuals, both
believed to be heterozygous, were crossed. Among the progeny, 30 have normal wings and 18
have vestigial wings. Carry out the chi-squared (2) test to find the probability of the results deviating
significantly by chance from the expected 3:1 ratio. Show your working.

Solution

1. H0: There is no difference from the 3: 1 ratio (i.e. parents are indeed heterozygous and
offspring phenotypic ratio is 3: 1)

HA: There is difference from the 3: 1 ratio (i.e. parents are not heterozygous and offspring
phenotypic ratio is not 3: 1)

2. Expected number of Drosophila with normal wings = 3/4 x 48 = 36

Expected number of Drosophila with vestigial wings = 1/4 x 48 = 12

(O - E)2 (30-36) 2 (18-12) 2 (-6) 2 (6) 2

3. 2calc =  = + = + = 4.0
E 36 12 36 12

Degrees of Probability (p)

freedom
4. (a) Degree of freedom (df) = 2 – 1 = 1 0.9 0.5 0.1 0.05 * 0.01 **
1 0.02 0.46 2.71 3.84 6.63
(b) Level of significance, α = 0.05 2 0.21 1.39 4.61 5.99 9.21
3 0.58 2.37 6.25 7.81 11.34
(c) 2 crit, df=1, =0.05 = 3.84 4 1.06 3.86 7.78 9.49 13.28
5 1.61 4.35 9.24 11.07 15.09

5. Since 2calc (= 4.0) is greater than 2 crit (= 3.84), the probability that chance alone is the reason
for the difference between observed results and the expected 3: 1 ratio is less than 5%. The
deviation is significant. Hence, reject H0 in favour of HA.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 26

 Worked Example 6: Colour of Petals in Plants

Two pure-breeding lines of plants, one with yellow petals and one with red petals were crossed. The
F1 are all orange. When the F1 are selfed, 320 plants are produced in the F2 generation in the
proportion of 182 orange petals: 61 yellow petals: 77 red petals.

There are at least two possibilities for the above ratios.

Carry out the chi-squared (2) test to find test the probability that either of the two explanations is
true. Show your working.

Solution

Possibility 1 Possibility 2
Incomplete dominance (1:2:1 phenotypic ratio) Recessive epistasis of allele r on alleles Y/y
(9:3:4 phenotypic ratio)
1. 1.
H0: There is no difference from the 1: 2: 1 ratio H0: There is no difference from the 9: 3: 4 ratio
HA: There is difference from the 1: 2: 1 ratio HA: There is difference from the 9: 3: 4 ratio
2. 2.
Expected number of orange petals = 2/4 x 320 = 160 Expected number of orange petals = 9/16 x 320 = 180
Expected number of yellow petals = 1/4 x 320 = 80 Expected number of yellow petals = 3/16 x 320 = 60
Expected number of red petals = 1/4 x 320 = 80 Expected number of red petals = 4/16 x 320 = 80
3. 3.

2calc = 2calc =

(O - E)2 (182-160) 2 (61-80) 2 (77-80) 2  (O - E)2 = (182-180) 2 + (61-60) 2 + (77-80) 2

 = + +
E 160 80 80 E 180 60 80
= 7.6 = 0.15

4. 4.
(a) df = n - 1 = 3 - 1 = 2 (a) df = n - 1 = 3 – 1 = 2
(b) Level of significance, α = 0.05 (b) Level of significance, α = 0.05
(c) 2 crit, df=2, =0.05 = 5.99 (c) 2 crit, df=2, =0.05 = 5.99
5. 5.
Since 2calc
(= 7.6) is GREATER than 2
crit (= 5.991), the Since 2calc (= 0.15) is SMALLER than 2 crit (= 5.991),
probability that chance alone is the reason for the difference probability that chance alone is the reason for the difference
between observed results and the expected 1:2:1 ratio is between observed results and the expected 9:3:4 ratio is
less than 5%. The deviation is significant. Hence, reject H0 more than 5%. The deviation is not significant and we can
in favour of HA. assume that it is recessive epistasis. Hence, do not reject
H0.
Explanation (FYI): Explanation (FYI):
• Looking along the 2-df row of the 2 probability table, we • The probability value (for df= 2) this time is greater than
find that the 2calc value places the probability at about 0.9, or 90%. Hence deviations from expected due to
0.025, or 2.5%. chance alone are expected approximately 90% of the
• This means that, if the hypothesis is true, then time, in other words, very frequently.
deviations from expectations due to chance alone are
expected approximately 2.5% of the time. • As 90 % is greater than 5 %, we conclude that the
results uphold the hypothesis of recessive epistasis.
• By convention the 5% level is used as the cut-off point.
When values of less than 5% are obtained, the
hypothesis is rejected as being too unlikely. Hence the
incomplete dominance hypothesis must be rejected.

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 27

 CONCEPT CHECK 3

Adapted from N02/P2/Q5

Pure-breeding pigmented mice were crossed with pure-breeding unpigmented mice. Their offspring,
which were all pigmented, were inter-crossed to produce 200 mice. In the F2 generation, the actual
numbers were 141 pigmented and 59 unpigmented mice.

(a) Carry out the 2 test to find the probability of the results departing significantly by chance from
an expected 3: 1 ratio. Show your working. [4]

Distribution of 2
Degrees of Probability
freedom 0.50 0.10 0.05 0.02 0.01 0.001
1 0.46 2.71 3.84 5.41 6.64 10.83
2 1.39 4.61 5.99 7.82 9.21 13.82
3 2.37 6.25 7.82 9.84 11.35 16.27
4 3.86 7.78 9.49 11.67 13.28 18.47

1. H0:

HA:

2.

3. 2calc =

4(a) df =

4(b) Level of significance, α =

→ Probability =

(b) Explain how the value for the 2 test from these results supports the genetic hypothesis of a
pair of segregating alleles at a single locus. [2]

HWA CHONG INSTITUTION / 2022-2023 H2 BIOLOGY / Core Idea 2 / Inheritance II 28