Selale University (SLU) Department of Biology: Quantitative Genetics (BIOL-6124)

Selale University (SLU)
Department of Biology
Quantitative Genetics (BIOL-6124)
5 ECTS; 2 conventional credit
Fekadu Gadissa (PhD)
Selale University (SLU) 1

Course Contents
1. Mendel’s Laws of Inheritance and Beyond
2. Population Structure and Population Genetics
3. Continuous Variation
4. Heritability
5. Selection
6. Inbreeding and Crossbreeding
7. Mating Designs and Estimation of Genetic Parameters
8. Genomic selection (GS)

Course Objective:
To introduce basic concepts in quantitative genetics
Learning outcome:
Understanding the basic concepts, theory and methods in quantitative genetics
with emphasis in applications for breeding programs
Understanding the fundamental genetic principles governing variation of

quantitative traits in populations
Developing quantitative and critical thinking abilities;

 Applying statistical analysis for genetic experiments
Analyzing quantitative genetic data, interpret and communicate results..
Evaluation:
Test, seminar paper, Final Exam

Unit 1
Mendel’s Laws
of Inheritance and Beyond

Brain storming questions
1. How do you define genetics?
2.What are the main themes of pre-mendelian, Mendelian and Post-Mendelian
genetic theories?
3.What does Mendelian laws of inheritance tell us?
4.Are all those Mendelian laws always true in natural populations?

1.1 Introduction
 Mendel's Laws of inheritance states that:
Adults are diploid; gametes are haploid
Each trait is controlled by a single gene
Each gene has two alternative forms called alleles
One allele is completely dominant over the other
All gametes are equally viable
Mating is always random
All offspring are equally viable
Genotype always determines phenotype
 Hence Mendel observed a 3:1 phenotypic ratio when two heterozygotes

(dihybrids) are crossed
 However, there are cases where these assumptions are violated
For example: under the following condition;

Sex Linkage  Pleiotropy (one gene-
Multiple allelism many character)
Codominance  variable expressivity
Incomplete dominance  incomplete penetrance
Polygenics  Environmental effects
Genetic interactions between non-  Lethal alleles
allelic genes on different loci/Epistasis  Linkage

(many gene-one character)

1.2 Non-Mendelian patterns of inheritance
1. Incomplete Dominance
•No allele is completely dominant over the other
•Dominant allele is unable to completely hide the effect of the recessive allele
•F1 does not resemble either parent
•Ex. Red snapdragons (Mirabilis jalapa) (RR) x White snapdragons (WW) result in
an F1 generation that is pink (RW)
•Produces 3 possible phenotypes with only two alleles
 More common in plants than in animals

Observe the color of the offspring that you would get on crossing a
pure (homozygous) red snapdragon with a pure white snapdragon
Selale University
9 (SLU)
Ans. They produce pink (neither red nor white) colored offspring
Hence, snapdragon flower color is

controlled by incompletely dominant
alleles and a new 3rd phenotype is seen

• Alleles that are incompletely dominant are written using a superscript letter.
• For example, flower color:
CWCW (white) plant X CRCR (red) plant……......P1
all CRCW (pink) offspring ……………F1
Ques:- What would happen to the phenotypic and genotypic ratios of the
offspring on selfying F1 progenies?

Incomplete Dominance
Gametes
CR CW
CRCR
CR
CRCR CRCW
Gametes
CW
F1 generation
All CRCW CRCW CWCW
F2 generation
CWCW 1:2:1
Selale University (SLU)

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 12
2. Co-dominance
 The condition in which both alleles, in a heterozygous organism, are expressed
(BOTH alleles contribute to the phenotype)
♣ It is characterized by full expression of both alleles in the
heterozygote
♣ However, the expression of both alleles does not have to be equal.
♣ The resulting phenotype consists of the phenotypes normally
associated with both alleles, i.e., not a watered down version of one
(as one sees with incomplete dominance)

Examples:
•ABO blood group- where A and B are codominant to each other
•Roan cattle (RW) – cross from a red and a white cow, have both red and
white hairs. NO PINK COWS!
•Sickle Cell Disease – caused by a 1 base pair change in the gene coding
for hemoglobin. Causes red blood cells to elongate into a sickle shape.
Very common in African-Americans (about 1 in 10 are carriers).
• Carriers have both normal and sickle red blood cells, and have
more normal RBC’s.
• Homozygous Sickle Cell have only sickle shaped RBC.

Summary
Co-dominance – When BOTH alleles are expressed
+ 
Incomplete dominance – When a BLEND of both

traits is resulted
+ 

3. Over-dominance
• Is the phenomenon in which a heterozygote is more vigorous than both of the
corresponding homozygotes
• Is also called heterozygote advantage
• Example = Sickle-cell anemia
• Autosomal recessive disorder
• Affected individuals produce abnormal form of hemoglobin
• Two alleles
• HbA  Encodes the normal hemoglobin, hemoglobin A
• HbS  Encodes the abnormal hemoglobin, hemoglobin S

4. Essential and Lethal Alleles
• Essential genes are those that are absolutely required for survival (for life)
• The absence of their protein product leads to a lethal phenotype
• It is estimated that about 1/3 of all genes are essential for survival
• A lethal allele is one that has the potential to cause the death of an organism
• These alleles are typically the result of mutations in essential genes
• They are usually inherited in a recessive manner
• Many lethal alleles prevent cell division
• These largely kills an organism at an early age
• Some lethal alleles exert their effect later in life

• Huntington disease

• Characterized by progressive degeneration of the nervous system,
dementia and early death
• The age of onset of the disease is usually between 30 to 50
• Dominant
• Dominant lethal alleles: not passed on through pedigrees OR have

late onset – Why?
• If recessive, Mendelian ratio not affected – why?
• If dominant, Mendelian ratio changes – why?
• Example: Dominant “creeper” allele in chickens

• Dominant lethal alleles result in the death of both homozygotes and
heterozygotes
• Recessive lethal alleles cause death only when homozygous
• An example of lethality is the yellow body color gene in mice
Lethal alleles
• Lethal alleles may produce ratios that seemingly deviate from Mendelian ratios
• e.g., “Creeper” phenotype in chickens
• Shortened wings and legs
• Creeps rather than walking normally

• All “creeper” birds are heterozygous
• Creeper x creeper  2:1 creeper : normal ratio
• Creeper allele is a recessive lethal
• Creeper homozygotes are

dead
• Effects of this allele
• Dominant for the creeper

phenotype
• Recessive for death

5. Multiple Allelism
A phenomenon where by a gene can have three or more alleles with in a
population
 In traits with multiple alleles, each individual can carry any two of the several
possible alleles.

1.3 Categories of genetic studies
1. Qualitative characters
•Refers to characters that could be grouped into , kinds, types/classes.
2. Quantitative Genetics
•Is a field of science involving transmission, inheritance or heredity of variations of

quantitative traits in individuals
•i.e. variation in traits that can only be differentiated using measurements.
3. Molecular studies
•Deals with biochemical and molecular mechanisms by which hereditary information is

stored in DNA (deoxyribonucleic acid) and subsequently transmitted to proteins.
•DNA is the molecule that stores genetic information within the cell.

Brain storming question
Discuses the following questions in your group and reflect the point of your
discussion to the class
1. Mention other fields of genetic studies you know
2. How do you explain variations between or among individuals in a given
population?
3. What do you think of variation from genetics and biotechnology view point?

1.4 Variation and Quantitative Studies
Variations in individuals are either qualitative (discontinuous or Mendelian

variations) or quantitative (continuous)
Qualitative variations (differences) are distinct types with little or no intermediate

forms
Largely resulted from single locus
Quantitative variations are continuous variations and usually resulted from

interaction of several genes (loci)
Thus, polygenic
The differences could be in degree rather than in kind and/or quantitative

rather than qualitative

 Inheritance of such differences and its understanding is fundamental to evolution, genetics, and
breeding
 However, the methods of study differ from those employed in Mendelian genetics in two respects:
1. Since ratios cannot be observed, single progenies are uninformative because
of inability to get ratios and thus, the unit of study must be extended to
‘populations’,
2. the nature of quantitative differences to be studied requires the measurement, and not just
the classification, of the individuals.
• Thus, Mendelian genetics was extended into quantitative genetics and introduced new concepts
connected with the genetic properties of ‘populations’ and the inheritance of measurements.

• Quantitative characters cannot be studied on individual basis, but rather on the
individuals in a population, or on all individuals in the population.
Characteristics of Quantitative Traits
1. They are largely normally distributed
2. They bear low heritablity
3. Controlled by many genes (polygenes)
4. Every allele has small contribution to a given phenotype
5. Their effects are greatly influenced by environment
6. Dominance (allelic-interaction) can obscure the true genotype effects
7. Environmental variation and the interaction of genotype with environment

obscure genetical effects
8. Epistasis (non-allelic interaction) would impose limitation to make prediction,
for example, predicted response to selection.
1.5 Development of Quantitative Genetics
• Johannsen, 1903, determined seed weight of inbred lines

• Variation among lines being heritable
• Parents with heavy lines gave heavy offsprings
• Variation within lines, not heritable, environmental
• Nilsson-Ehle in 1909 studied kernel color in wheat

• crossed red lines to white
• F1 red intermediate between the two parents, and
• F2 ranged from red to white.
• Some lines segregated 3:1 (red:white) in the F2,

• whereas some segregated 15:1 and some 63:1.
• Kernel color is ontrolled by three genes.
• Those three genes act additively independently that gives a continuous

distribution
• Fisher (1918) introduced statistics in Mendelian genetics, where variance (2)

was used to measure differences in a population.
This analysis involves population, not an individual.
Population - Group of individuals belonging to a certain class.
• Wright (1932) studied coat color in guinea pigs and recognized the importance
of gene interaction
Inbreeding, non-random mating and selection on the genetic composition of a

population.
• The two most important contribution of Wright are the concept of inbreeding
coeficient and effective population size.
• Mather in 1942 demonstrated the polygenic nature of quantitative characters

through estimating effects of gene action,
• He concluded that qualitative traits are controlled by major genes, whereas

quantitative traits are controlled by minor genes with cummulative effects.
• 1940s - basic principles of gene action and gene to gene relationship
• 1950s - mating designs, Comstock and Robinson (diallel and NC designs)
• 1960s - biometrical genetics, diallel, etc.
• 1970s - more developments in biometrical procedures
• 1980s to present - tie up biometrical genetics with plant physiology and

molecular mechanisms, now QTL mapping.
1.6 Importance of Quantitative Genetics
1. Used to study economically important traits in:
Crops, Livestock, Micro-organisms etc.
2. Quantitative traits are controlled by many genes, and greatly influenced by

environmental factors.
Therefore, it is important to know how much (percentage) of the variation is

heritable and how much is not.
Such information is important in selection of traits in breeding and selection

program.
3. Important in evolution studies.
4. Important in population studies.

Unit 2
Population Structure and Population Genetics

• In quantitative genetic studies, information on the population is more important
than that of an individual.
• Although it is controlled by polygenes, gene transmission follows the principles of

Mendel's Law, but more complicated in its computations.
2.1 Gene Transmission
 For individuals that are sexually propagating, gene transmission from parents to
progenies happen through the gametes.
 Gametes are formed through the process of meiosis (gametogenesis), following

which, they then undergo fusion or fertilisation to form individuals (zygotes).
Q) Brief Meiosis
 To ensure the formation of normal proportion of genotypes in the progeny

generation, the following should be true:
1. Meiosis/gametogenesis should occur normally and complete
- no problem of abnormal gametes
- no problem of lethal alleles
2. Mating should occur at random
- no unidirectional mating
3. No problem of genotype lethality

2.2 Gene and genotypic frequencies
•Specification of genotypes is important in describing the genetic constitution of a

group of individuals
•For example: An autosomal locus A having A1 and A2 alleles would possess three
different genotypes such as A1A1, A2A2, and A1A2
• Population, in the genetic sense, is not just a group of individuals, but a breeding
group
•Thus, population genetics is concerned with the genetic constitution of the

individuals and transmission of the genes from one generation to the next.
•Random mating is essential

• In random mating population, every individual in the population has the same
probability (chance) to mate with every other individual in the population.
• Random mating is also called panmixia, while the population involved is called a
panmictic population.
• In a panmictic population, panmixia usually only occurs in large populations -

with hundreds or thousands of individuals.
For example;
Gene (allele) Genotype (allelic combination)
________________________________
A a AA Aa aa
Freq p q P H Q

With random mating,
AA Aa aa
P H Q
__________________________________
AA P P2 PH PQ
Aa H PH H2 HQ
aa Q PQ HQ Q2
As a result of panmixia, progenies with the following proportions are obtained:
Mating Frequency Progeny Genotype Frequency
_________________________________________________
AA Aaaa
_____________________________________________________________________________
AA x AA P2 P2 - -
AA x Aa 2PH PH PH -
AA x aa 2PQ - 2PQ -
Aa x Aa H 2 1/4H 2 1/2H 2 1/4H2
Aa x aa 2HQ - HQ HQ
aa x aa Q2 - - Q2
_____________________________________________________________________________
Total 1 (P + 1/2H)2 2(P + 1/2H)(Q + 1/2H) (Q + 1/2H)2
p2 2pq q2
____________________________________________________________________________
The gene frequencies in this population are:
p = P + 1/2H = p2 + 1/2 (2pq)
= p2 + pq
= p (p + q)
=p
q = Q + 1/2H = q2 + 1/2(2pq)
= q2 + pq
= q(p + q)
=q
• This shows that, in a panmictic population, gene and genotype frequencies

remain constant.

 During transmission, the genotypes of the parents are broken down and thus, a
new set of genotypes is constituted in the progeny.
 The genes carried by the population thus have continuity from generation to
generation, but the genotypes in which they appear do not.
 The genetic constitution of a population, referring to the genes it carries, is

described by the array of gene frequencies
 Gene frequency refers to specification of the alleles and numbers of proportions

of the different alleles present at every locus
 If, for example, A1 is an allele at the A locus, the frequency of A1 genes is the
percentage of all genes at this locus that are the A1 alleles.

• The frequencies of all the alleles at any one locus must add up to unity (100%).
• The gene frequencies at a particular locus among a group of individuals can be

determined from a knowledge of the genotype frequencies.
• To take a hypothetical example, suppose there are two alleles, A1 and A2, and we
classify 100 individuals and count the numbers in each genotype as follows:
• Since each individual contains two genes, 200 representatives of the genes have
counted at the locus.
• Each A1A1 individual contains two A1 genes and each A1A2 contains one A1 gene.

• So there are 120 A1 genes in the sample, and 80 A2 genes.
• The frequency of A1 is therefore 60 per cent or 0.6, and the frequency of A2 is 40

per cent or 0.4.
• To express the relationship in a more general form, let the frequencies of genes
and of genotypes be as follows:
• Thus, p + q = 1 and P + H + Q = 1
• Each individual contains two genes

• Thus, the relationship between gene frequency and genotype frequency among the
individuals counted is presented as follows:
p = P + 1/2H ; q = Q + 1/2H
• Allelic variation for discrete traits, whether phenotypically visible or cryptic, is

known as polymorphism
• Polymorphic loci give rise to the variation in quantitative characters, which is

the subject of this course.
2.3 Causes of change
• To understand quantitative genetic variations, information on causes of gene and

genotype frequencies are important
• Several factors are responsible for the variations.
• Some are:
A. Population size:
The genes passed from one generation to the next are a sample of the genes in the
parent generation.
•Therefore the gene frequencies are subject to sampling variation between

successive generations,
•The smaller the number of parents the greater is the sampling variation.
B. Differences in fertility and viability:
The different genotypes among the parents may have different fertilities, and if
they do they will contribute unequally to the gametes out of which the next
generation is formed.

2.4 The Hardy-Weinberg principle
Home take question

 Briefly describe what Hardy-Weinberg refers to
 Discuss how it affects genetic variation
States that gene and genotype frequencies in the population remain constant
from one generation to another
The principle holds trure if there is no purturbing forces
It is one of the most important principles of population genetics
It was formulated independently by both Godfrey H. Hardy and Wilhelm

Weinberg in 1908
It is a mathematical model that provides a framework for understanding how

populations evolve
Hardy-Weinberg predictions
Allelic and/or genotypic frequencies of a population remain constant after one

generation if the Hardy-Weinberg assumptions are met (if there is no perturbing
forces).
The formula was built considereing;
♣ large and panmictic population
♣ one locus (unlinked gene)
♣ absence of migration, mutation and selection
It is designated by the formula:
p2 + 2pq + q2 = 1
where p and q represents frequencies of both alleles at a given locus
 The prediction and formula is further elaborated assuming a diploid,
autosomal locus with 2 alleles:
 For example, in parents with A and a alleles;
 A large gamete pool (gene pool) containing alleles A and a would be

produced
aAAa
aAAaAaa
aAAaaAaAA
aaAAaaa
aAaaAA
AaA

Thus, gamete (allele) frequencies would be:
If Freq(A) = p
Freq(a) = q
 p+q=1
Genotype frequencies of 3 possible zygotes:

AA,Aa, aa
Freq (AA) = pA x pA = pA2
Freq (Aa) = (pA x qa) + (qa x pA) = 2pAqa
Freq (aa) = qa x qa = qa2
 p2 + 2pq + q2 = 1 Selale University (SLU) 47

If you are give genotype frequencies, you can use the
following relationship to compute allelic frequencies:
Genotypes: AA, Aa, aa
Frequency: p2 2pq q2
Frequency of the A allele:

p = p2 + ½ (2pq)
Frequency of the a allele:

q = q2 + ½ (2pq) Selale University (SLU) 48
Hardy-Weinberg assumptions:
Hardy-Weinberg laws was set on the bases of the following assumptions:
1) Mating is random (no sexual selection)
2) The population is infinitely large. (no sampling error or genetic drift)
3) Genes are not added from outside the population (no gene flow or migration)
4) Genes do not change from one allelic state to another (no mutation)
5) All individuals have equal probabilities of survival and reproduction (no natural
selection)

Conclusions on the Hardy-Weinberg principle
1) A random mating population with no external forces will reach the equilibrium
in a single generation, and these frequencies remain constant there after
2) Any perturbation of the gene frequencies leads to a new equilibrium after
random mating
3) The amount of heterozygosity is maximized when the gene frequencies are
intermediate
i.e 2pq has a maximum value of 0.5 when p = q = 0.5

GENOTYPE VERSUS GENE FREQUENCIES
p (AA)
2 q2 (aa)
2pq (Aa)

Or alternatively

Summary question
Two co-dominant alleles such as LM and LN are involved in blood

group inheritance of human population. If you are given a record of the
following MN blood groups;
Blood groups Blood genotypes Record
MM LMLM 364
MN LMLN 344
NN LNLN 44
Using MN locus, calculate a) the allelic frequencies
b) the genotypic frequencies

Importance of the Hardy-Weinberg principle
1) Enables us to compute genotype frequencies from generation to

generation, even with selection
2) Serves as a null model in tests for natural selection, nonrandom
mating, etc., by comparing observed to expected genotype
frequencies
3) Forensic analysis
4) Expected heterozygosity provides a useful means of summarizing
the molecular genetic diversity in natural populations

Effect of Multiple Allelisim
In some situations, there are more than two alleles on a locus.
 In this case, the population will reach equilibrium after one generation of random
mating.
This can be shown either by
- random mating of gametes, or
- random mating of genotypes

Assuming the case of three alleles on one locus: A, a' and a
Gene Genotype
A a’ a AA Aa’ Aa a’a’ a’a aa
f p q r p2 2pq 2pr q2 2qr r2

After random mating of gametes, the change would be:
A a’ a
p q r
A p AA p2 Aa’ pq Aa pr
a’ q Aa’ pq a’a’ q2 a’a qr
a r Aa pr a’a qr aa r2
Inference:
Genotype AA Aa’ Aa a’a’ a’a aa
Frequency p2 2pq 2pr q2 2qr r2
P Q R S T U

pA = 2P + Q + R = 2P + Q + R
2(P + Q + R + S + T + U) 2
= P + 1/2Q + 1/2R
= p2 + 1/2(2pq) + 1/2(2pr)
= p2 + pq + pr
= p(p + q + r)
=p
q a’ = S + 1/2Q + 1/2T
= q2 + 1/2(2pq) + 1/2(2qr)
= q2 + pq + qr
= q(q + p + r)
=q
ra = U + 1/2R + 1/2T
= r2 + 1/2(2pr) + 1/2(2qr)
= r2 + pr + qr
= r(r + p + q)
=r
Discuss the effects of multiple genes that have no normal differentiation

and Sex linkage on HW equilibrium
2.4 Changes of Gene Frequency
• Changes in gene frequency, and consequently of genotype frequencies, are

brought about by two major process: systematic processes, and dispersive process.
• Systematic processes tend to change the gene frequency in a manner predictable

both in amount and in direction;
• Dispersive process arises in small populations from the effects of sampling, and is
predictable in amount but not in direction.
A. Systematic processes:
• There are three systematic processes: migration, mutation, and selection.
Migration
• Migration refers to arrival of individuals from somewhere else or outgoing of

individuals to another group. Selale University (SLU) 59
For example:
•Consider a given large population consisting of new immigrants with a proportion

m (migration rate) in each generation, the remainder, 1-m, being natives.
•Let the frequency of a certain gene be qm among the immigrants and q0 among the
natives.
•Then the frequency of the gene in the mixed population, q1 will be
•The change of gene frequency, ∆q, brought about by one generation of

immigration is the difference between the frequency before immigration and the
frequency after immigration. Therefore,
• It can therefore be concluded that the change in gene frequency in the new
population depends on:
• migration rate, and
• the difference in gene frequencies between the immigrants and the natives.

Mutation
•The effect of mutation on the genetic properties of the population differs

according to mutational event or mutational step.
•Suppose gene A1 mutates to A2 with a frequency u per generation.
•Then, the frequency of A1 in one generation is p0, and the frequency of newly
mutated A2 genes in the next generation is up0.
•So the new gene frequency of A1 is p0 — up0, and the change of gene frequency is
-up0.
•If the genes mutate in both directions, then;

• Then the change of gene frequency in one generation is:
• The point of equilibrium can be found by equating the change of frequency, ∆q
to zero and thus,

Selection
•Individuals differ in viability and fertility, and thus contribute different numbers of
offspring to the next generation.
•The contribution of offspring to the next generation is called fitness or adaptive

value, or selective value.
•If the differences of fitness are associated with the presence or absence of a
particular gene in the individual’s genotype, then selection operates on that gene.
•As a result, its frequency differs in the offspring and the parents.
•The strength of selection is expressed as the coefficient of selection, s,
•S is expressed as the proportionate reduction in the gametic contribution of a

particular genotype compared with a standard genotype, usually the most favored.

• Accordingly, the contribution of the favored genotype is taken to be 1, and the
contribution of the genotype selected against is then 1 - s.
• This expresses the fitness of one genotype relative to the other.
• Suppose, the coefficient of selection is s = 0.1; the fitness is then 0.9, which
means that for every 100 zygotes produced by the favored genotype, only 90 are
produced by the genotype selected against.
Change of gene frequency under selection
• In a given genotypes A1A1, A1A2 and A2A2, if A2A2 is the recessive
homozygote with a coefficient of selection s acting against it; then the new gene
frequency after selection could be given as;

•The change of gene frequency, ∆q, resulting from one generation of selection is
∆q = q1 –q
•Substituting for q1 from the above equation;
•The formula indicate that the effect of selection on gene frequency depends not
only on the intensity of selection s, but also on the initial gene frequency.

• Expressions and frequency of the new gene basically differs with different
conditions of dominance (see below)

Polymorphism
•Refers to existence of allelic variants at a given locus with a frequencies too high
to be accounted for by selection-mutation balance.
•Operationally, a polymorphic locus is usually defined as one for which the

frequency of the most common allele is less than 0.99.
•Polymorphism is found in almost all natural populations, and occurs at all levels of
genetic organization (from DNA sequences to major morphological traits).
•The amount of variation differs for different kinds of trait.
•Its extent is measured in terms of the frequency of heterozygotes, H.
•H can be expressed as an observed value, or as an expected value calculated from

the observed gene frequencies.

Group discussion
How do you elaborate the variations (polymorphisms) in terms

of:
a) morphological traits
b) Isozyme data
b) molecular markers data

B. Dispersive process
•It is assumed that in the absence of migration, mutation, or selection, the gene and
genotype frequencies remain unaltered from generation to generation.
•However, the stability does not hold in a small population, because of random
fluctuations arising from the sampling of gametes.
•Such random change of gene frequency is the dispersive process and the most
known are:
1. Random drift:
 Refers to the random changes of gene frequency.
It cause a gene frequency change in an erratic manner from generation to

generation, with no tendency to revert to its original value.

2. Differentiation between sub-populations
•Random drift occurring independently in different sub-populations leads to genetic

differentiation between the sub-populations.
•The inhabitants of a large area seldom in nature constitute a single large

population, because restricted mating between inhabitants of the same region.
•Natural populations are therefore more or less subdivided into local groups or sub-
populations, and these come to differ in gene frequencies if the number of
individuals in the groups is small.
3. Uniformity within sub-populations
Genetic variation within each sub-population becomes progressively reduced, and

the individuals become more and more alike in genotype.
This genetic uniformity is common in lab organisms or in a very small population

4. Increased homozygosity due to inbreeding
Homozygotes increase in frequency at the expense of heterozygotes.
This, coupled with the general tendency for deleterious alleles to be recessive, is the
genetic basis for the loss of fertility and viability.
•There are two different ways of looking at the dispersive process and of deducing its
consequences:
variation in terms of a sampling process (sampling variance) and genotypic
changes resulting from mating between related individuals (inbreeding).
Variance in gene frequency due to sampling
•The change in gene frequency due to sampling is a random event so that its direction is
unpredictable.
•But its magnitude can be predicted in terms of the variance of the change.
• In the formation of lines from the base population, each line is formed from a
sample of N individuals drawn from the base population.
• Since each individual carries two genes at a locus, the subdivision of the population
represents a series of samples each of 2N genes, drawn at random from the base
population.
• The gene frequencies in these samples will have an average value equal to that in the
base population, i.e. qo, and will be distributed about this mean with a variance po
qo/2N
• This is the variance of q1, the gene frequency in the different lines after one
generation.
• Since the initial gene frequency qo is the same for all lines, it is also the variance of
(q1 — qo), which is the change of gene frequency.
Thus, the change of gene frequency, ∆q, resulting from sampling in one generation,
could be stated in terms of its variance as:
•Such variance of ∆q expresses the magnitude of the change of gene frequency

resulting from the dispersive process.
Fixation
•There are limits to the spreading apart of the lines that can be brought about by the
dispersive process.
•The gene frequency becomes 0 or 1 at this limit and thus, ‘traps’ or points of no
return.
 Thus, fixation refers to gaining an allele frequency of 1 at a given locus. On the
contrary, if the frequency becomes 0, the allele becomes lost
 When a line is fixed, all individuals in it are of identical genotype with respect to
that locus. Eventually all lines, and all loci in a line, become fixed.
 The individuals of a line are then genetically identical, and this is the basis of the
genetic uniformity of highly inbred strains.
• When all lines are fixed, the mean gene frequency remain unchanged and equal to
the initial gene frequency.
• For example: if the base population contains two alleles A1 and A2 at frequencies
po and qo respectively, then A1 will be fixed in the proportion po of the lines, and
A2 in the remaining proportion qo .
• The variance of the gene frequency among the lines is then po qo

2.5 Genotype frequencies in small population
•Change of gene frequency leads to change of genotype frequencies
•Thus, genotype frequencies in small populations follow the changes of gene

frequency resulting from the dispersive process.
•In the idealized population, mating is random within each of the lines. Consequently
the genotype frequencies in any one line are the Hardy-Weinberg frequencies
appropriate to the gene frequency in the previous generation of that line.
•As the lines drift apart in gene frequency, they become differentiated also in
genotype frequencies.
•But differentiation is not the only aspect of the change: the general direction of the
change is toward an increase of homozygous, and a decrease of heterozygous,
genotypes.
• The genotype frequencies in the population as a whole can be deduced from a
knowledge of the variance of gene frequencies.
• Thus, if an allele has a frequency q in one particular line, homozygotes of that

allele will have a frequency of q2 in that line.
• The frequency of these homozygotes in the population as a whole will therefore

be the mean value of q2 over all lines.
• The value of (q2) can be found from a knowledge of the variance of gene
frequencies among the lines
• In such case, the variance of a set of observations is found by deducting the

square of the mean from the mean of the squared observations. Thus

• Since the mean gene frequency is equal to the original qo, the genotypic frequencies for a locus
with two alleles is given as follows:
• These genotype frequencies are no longer the Hardy-Weinberg frequencies appropriate to the
original or mean gene frequency.
Inbreeding
• Inbreeding means the mating together of individuals that are related to each other by ancestry.
• Pairs mating at random are more closely related to each other in a small population than in a
large one.

• Two genes that have originated from the replication of one single gene in a
previous generation may be called identical by descent, or simply identical.
• Two genes that are not identical are independent in descent.
• Identity by descent provides the basis for a measure of the dispersive process,
through the degree of relationship between the mating pairs.
• The measure is the coefficient of inbreeding, which is the probability that the two
genes at any locus in an individual are identical by descent.
• It refers to an individual and expresses the degree of relationship between the

individual’s parents.
• If the parents of any generation have mated at random then the coefficient of
inbreeding of the progeny is the probability that two gametes taken at random
from the parent generation carry identical genes at a locus.
This is the average coefficient of inbreeding of all the progeny.
•The coefficient of inbreeding is generally symbolized by F.
•The degree of relationship expressed in the inbreeding coefficient is essentially a

comparison between the population in question and some specified or implied base
population.
•In a population having N individuals, there are 2N different sorts at each locus.
•Thus, any gamete had a (l/2N)th chance of uniting with another of the same sort.
•So, 1/2N is the probability that uniting gametes carry identical genes, and is thus
the coefficient of inbreeding of the progeny.
•In the second generation, homozygotes could arise in two ways : one from the new
replication of genes and the other from the previous replication.

 Thus, the probability of newly replicated genes coming together in a zygote is
again 1/2N.
 The remaining proportion, 1 — 1/2N, of zygotes carry genes that are independent
in their origin from generation 1, but may have been identical in their origin from
generation 0 (base population).
• Thus the total probability of identical homozygotes in generation 2 is:
where F1 and F2 stand for the inbreeding coefficients of generations 1 and 2 respectively.
• The same argument applies to subsequent t generations and is given by:

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Selale University (SLU)

Quantitative Genetics (BIOL-6124)

5 ECTS; 2 conventional credit

Fekadu Gadissa (PhD)

Selale University (SLU) 1

1. Mendel’s Laws of Inheritance and Beyond

2. Population Structure and Population Genetics

6. Inbreeding and Crossbreeding

7. Mating Designs and Estimation of Genetic Parameters

8. Genomic selection (GS)

Selale University (SLU) 2

To introduce basic concepts in quantitative genetics

Understanding the fundamental genetic principles governing variation of

Developing quantitative and critical thinking abilities;

Test, seminar paper, Final Exam

Selale University (SLU) 4

1. How do you define genetics?

2.What are the main themes of pre-mendelian, Mendelian and Post-Mendelian

3.What does Mendelian laws of inheritance tell us?

4.Are all those Mendelian laws always true in natural populations?

Selale University (SLU) 5

Adults are diploid; gametes are haploid

Each trait is controlled by a single gene

Each gene has two alternative forms called alleles

One allele is completely dominant over the other

All gametes are equally viable

Mating is always random

All offspring are equally viable

Genotype always determines phenotype

 Hence Mendel observed a 3:1 phenotypic ratio when two heterozygotes

For example: under the following condition;

Multiple allelism many character)

Codominance  variable expressivity

Incomplete dominance  incomplete penetrance

Polygenics  Environmental effects

Genetic interactions between non-  Lethal alleles

allelic genes on different loci/Epistasis  Linkage

Selale University (SLU) 7

•No allele is completely dominant over the other

•F1 does not resemble either parent

•Produces 3 possible phenotypes with only two alleles

 More common in plants than in animals

Selale University (SLU) 8

Hence, snapdragon flower color is

Selale University (SLU) 10

• For example, flower color:

CWCW (white) plant X CRCR (red) plant……......P1

all CRCW (pink) offspring ……………F1

Selale University (SLU) 11

Selale University (SLU)

 The condition in which both alleles, in a heterozygous organism, are expressed

(BOTH alleles contribute to the phenotype)

♣ It is characterized by full expression of both alleles in the

♣ However, the expression of both alleles does not have to be equal.

♣ The resulting phenotype consists of the phenotypes normally

(as one sees with incomplete dominance)

Selale University (SLU) 13

Selale University (SLU) 14

Co-dominance – When BOTH alleles are expressed

Incomplete dominance – When a BLEND of both

Selale University (SLU) 15

• Example = Sickle-cell anemia

• Autosomal recessive disorder