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Linkage, crossing over and basic
microbial genetics
Cell biology and Genetics
Unit – 5
Mapping of gene
• Genome mapping, is the creation of a genetic map
assigning DNA fragments to chromosomes.
• Genetic linkage is the tendency of alleles that are
located close together on a chromosome to be
inherited together during meiosis. Genes whose loci
are nearer to each other are less likely to be separated
onto different chromatids during chromosomal
crossover, and are therefore said to be genetically
linked. In other words, the nearer two genes are on a
chromosome, the lower is the chance of a swap
occurring between them, and the more likely they are
to be inherited together.
Linkage map
• A linkage map is a genetic map of a species or
experimental population that shows the position
of its known genes or genetic markers relative to
each other in terms of recombination frequency,
rather than a specific physical distance along each
chromosome.
• Linkage mapping is critical for identifying the
location of genes that cause genetic diseases.
• A genetic map is a map based on the frequencies
of recombination between markers during
crossover of homologous chromosomes.
• The greater the frequency of recombination
(segregation) between two genetic markers, the further
apart they are assumed to be. Conversely, the lower the
frequency of recombination between the markers, the
smaller the physical distance between them.
• Historically, the markers originally used were detectable
phenotypes (enzyme production, eye color) derived
from coding DNA sequences; eventually, confirmed or
assumed non coding DNA sequences such as
microsatellites or those generating restriction fragment
length polymorphisms (RFLPs) have been used.
• Genetic maps help researchers to locate other markers,
such as other genes by testing for genetic linkage of the
already known markers.
• A genetic map is not a physical map (such as a radiation
reduced hybrid map) or gene map.
Genome sequencing
• Genome sequencing are sometimes
mistakenly referred to as "genome mapping"
by non-biologists. While the scope, purpose
and process are totally different, a genome
assembly can be viewed as the "ultimate"
form of physical map, in that it provides all
information that a traditional physical map
can offer in a much better way.
Gene mapping
• The essence of all genome mapping is to place a collection of molecular
markers onto their respective positions on the genome.
• Molecular markers come in all forms. Genes can be viewed as one special
type of genetic markers in the construction of genome maps, and mapped
the same way as any other markers.
• In genetic mapping, any sequence feature that can be faithfully
distinguished from the two parents can be used as a genetic marker.
Genes, in this regard, are represented by "traits" that can be faithfully
distinguished between two parents.
• In physical mapping, there are no direct ways of marking up a specific
gene since the mapping do not include any information that concern traits
and functions. Genetic markers can be linked to a physical map by
processes in situ hybridization. By this approach, physical map contigs can
be "anchored" onto a genetic map.
Physical Mapping
• In physical mapping, the DNA is cut by a restriction enzyme. Once
cut, the DNA fragments are separated by electrophoresis. The
resulting pattern of DNA migration (i.e., its genetic fingerprint) is
used to identify what stretch of DNA is in the clone. By analyzing
the fingerprints, contigs are assembled by automated (FPC) or
manual means (Pathfinders) into overlapping DNA stretches. Now a
good choice of clones can be made to efficiently sequence the
clones to determine the DNA sequence of the organism under
study (seed picking).
• Macrorestriction is a type of physical mapping wherein the high
molecular weight DNA is digested with a restriction enzyme having
a low number of restriction sites.
• There are alternative ways to determine how DNA in a group of
clones overlap without completely sequencing the clones. Once the
map is determined, the clones can be used as a resource to
efficiently contain large stretches of the genome. This type of
mapping is more accurate than genetic maps.
Recombination
• The exchange of DNA sequences between
different molecules, occurring either naturally
or as a result of DNA manipulation.
• A process by which pieces of DNA are broken
and recombined to produce new
combinations of alleles.
What is gene cloning?
1 A fragment of DNA, containing the gene to be
cloned, is inserted into a circular DNA molecule
called a vector, to produce a recombinant DNA
molecule.
2 The vector transports the gene into a host cell,
which is usually a bacterium, although other
types of living cell can be used.
3 Within the host cell the vector multiplies,
producing numerous identical copies, not only of
itself but also of the gene that it carries.
4 When the host cell divides, copies of the
recombinant DNA molecule are passed to the
progeny and further vector replication takes
place.
5 After a large number of cell divisions, a colony,
or clone, of identical host cells is produced. Each
cell in the clone contains one or more copies of
the recombinant DNA molecule; the gene carried
by the recombinant molecule is now said to be
cloned.
1
Crossing Over
• (i) Crossing over is a recombination of genes due to
exchange of genetic material between two
homologous chromosomes,
• (ii) It is the mutual exchange of segments of genetic
material between non-sister chromatids of two
homologous chromosomes, so as to produce re-
combinations or new combinations of genes.
• The non-sister chromatids in which exchange of
segments have occurred are called recombinants or
cross-overs while the other chromatids in which
crossing over has not taken place are known as
parental chromatids or non cross-overs.
• Each parent cell has pairs
of homologous
chromosomes, one
homolog from the father
and one from the mother.
In meiosis, the maternal
and paternal
chromosomes can be
shuffled into the daughter
cells in many different
combinations (in humans
there are 223 possible
combinations!).
• This ensures genetic variation in sexually reproducing
organisms. Further genetic variation comes from
crossing over, which may occur during prophase I of
meiosis.
• In prophase I of meiosis, the replicated homologous
pair of chromosomes comes together in the process
called synapsis, and sections of the chromosomes are
exchanged. You can see that after crossing over, the
resultant chromosomes are neither entirely maternal
nor entirely paternal, but contain genes from both
parents. Synapsis and crossing over occur only in
meiosis.
Bacterial Sexual Processes
• Eukaryotes have the processes of meiosis to reduce diploids
to haploidy, and fertilization to return the cells to the diploid
state. Bacterial sexual processes are not so regular. However,
they serve the same aim: to mix the genes from two different
organisms together.
• The three bacterial sexual processes:
– 1. conjugation: direct transfer of DNA from one bacterial
cell to another.
– 2. transduction: use of a bacteriophage (bacterial virus) to
transfer DNA between cells.
– 3. transformation: naked DNA is taken up from the
environment by bacterial cells.
15
Transformation
• The essence of recombinant
DNA technology is to remove
DNA from cells, manipulate it
in the test tube, then put it
back into living cells. In most
cases this is done by
transformation.
• In the case of E. coli, cells are
made “competent” to be
transformed by treatment
with calcium ions and heat
shock. E. coli cells in this
condition readily pick up DNA
from their surroundings and
incorporate it into their
genomes.
16
2
Gene Transfer by Transformation
•Transformation is the process of importing free
DNA into bacterial cells.
• the cells need to be competent.
• Many cells are capable of natural Transformation
and naturally competent.
• others require artificial manipulations.
• Perturbing the membrane by chemical (CaCl2) or
electrical (electroporation) methods
• Not all bacteria can take up free or naked DNA
(<1%). 17
Gram positive Bacteria transform DNA using a
Transformasome complex
Gram-negative bacteria do not use transformasomes
18
3
Conjugation
• Physical contact between two bacteria, usually
associated with transfer of DNA from one cell
to the other.
Conjugation
• Conjugation is the closest analogue in bacteria to
eukaryotic sex.
• The ability to conjugate is conferred by the F
plasmid. A plasmid is a small circle of DNA that
replicates independently of the chromosome.
Bacterial cells that contain an F plasmid are called
“F+”. Bacteria that don’t have an F plasmid are
called “F-”.
• F+ cells grow special tubes called “sex pilli” from
their bodies. When an F+ cell bumps into an F-
cell, the sex pilli hold them together, and a copy of
the F plasmid is transferred from the F+ to the F-.
Now both cells are F+.
20
21
4
Hfr Conjugation
• When it exists as a free plasmid,
the F plasmid can only transfer
itself. This isn’t all that useful for
genetics.
• However, sometimes the F
plasmid can become incorporated
into the bacterial chromosome,
by a crossover between the F
plasmid and the chromosome.
The resulting bacterial cell is
called an “Hfr”, which stands for
“High frequency of
recombination”.
• Hfr bacteria conjugate just like F+
do, but they drag a copy of the
entire chromosome into the F-
cell.
• Technique used in bacterial gene
mapping
22
Intracellular Events in Conjugation
• The piece of chromosome that enters the F- form the Hfr is
linear. It is called the “exogenote”.
• The F- cell’s own chromosome is circular. It is called the
“endogenote”.
• Only circular DNA replicates in bacteria, so genes on the
exogenote must be transferred to the endogenote for the F-
to propagate them.
• This is done by recombination: 2 crossovers between
homologous regions of the exogenote and the endogenote. In
the absence of recombination, conjugation in ineffective: the
exogenote enters the F-, but all the genes on it are lost as the
bacterial cell reproduces.
23
F-prime (F’)
• The process of making an Hfr from an F+ involves a crossover between the
F plasmid and the chromosome. This process is reversible: an Hfr can
revert to being F+ when the F plasmid DNA incorporated into the Hfr
chromosome has a crossover and loops out of the chromosome forming
an F plasmid once again.
• Sometimes the looping-out and crossing-over process doesn’t happen at
the proper place. When this happens, a piece of the bacterial
chromosome can become incorporated into the F plasmid. This is called
an F’ (F-prime) plasmid.
• F’ plasmids can be transferred by conjugation. Conjugation with an F’ (or a
regular F plasmid) is much faster and more efficient than with an Hfr,
because only a very small piece of DNA is transferred. Since the F’ carries
a bacterial gene, this allele can be rapidly moved into a large number of
other strains. This permits its function to be tested rapidly. Also, tests of
dominance can be done.
• A cell containing an F’ is “merodiploid”: part diploid and part haploid. It is
diploid for the bacterial gene carried by the F’ (one copy on the F’ and the
other on the chromosome), and haploid for all other genes.
24
Transduction
• Transduction is the process of moving bacterial DNA from one
cell to another using a bacteriophage.
• Bacteriophage or just “phage” are bacterial viruses. They
consist of a small piece of DNA inside a protein coat. The
protein coat binds to the bacterial surface, then injects the
phage DNA. The phage DNA then takes over the cell’s
machinery and replicates many virus particles.
• Two forms of transduction:
– 1. generalized: any piece of the bacterial genome can be transferred
– 2. specialized: only specific pieces of the chromosome can be
transferred.
25
General Phage Life Cycle
• 1. Phage attaches to the cell
and injects its DNA.
• 2. Phage DNA replicates,
and is transcribed into RNA,
then translated into new
phage proteins.
• 3. New phage particles are
assembled.
• 4. Cell is lysed, releasing
about 200 new phage
particles.
• Total time = about 15
minutes.
26
EM of Bacteriophages
27
Generalized Transduction
• Some phages, such as phage P1, break up the bacterial
chromosome into small pieces, and then package it into some
phage particles instead of their own DNA.
• These chromosomal pieces are quite small.
• A phage containing E. coli DNA can infect a fresh host,
because the binding to the cell surface and injection of DNA is
caused by the phage proteins.
• After infection by such a phage, the cell contains an
exogenote (linear DNA injected by the phage) and an
endogenote (circular DNA that is the host’s chromosome).
• A double crossover event puts the exogenote’s genes onto the
chromosome, allowing them to be propagated.
28
Transduction Mapping
• Only a small amount of chromosome, a few genes,
can be transferred by transduction. The closer 2
genes are to each other, the more likely they are to
be transduced by the same phage. Thus, “co-
transduction frequency” is the key parameter used in
mapping genes by transduction.
• Transduction mapping is for fine-scale mapping only.
Conjugation mapping is used for mapping the major
features of the entire chromosome.
29
Mapping Experiment
• Important point: the closer 2 genes are to each other, the
higher the co-transduction frequency.
• We are just trying to get the order of the genes here, not put
actual distances on the map.
• Expt: donor strain is aziR leu+ thr+. Phage P1 is grown on the
donor strain, and then the resulting phage are mixed with the
recipient strain: aziS leu- thr-. The bacteria that survive are
then tested for various markers
• 1. Of the leu+ cells, 50% are aziR, and 2% are thr+. From this we
can conclude that azi and leu are near each other, and that
leu and thr are far apart.
• But: what is the order: leu--azi--thr, or azi--leu--thr ?
30
Mapping Experiment, pt. 2
• 2. Do a second experiment to determine the order.
Select the thr+ cells, then determine how many of
them have the other 2 markers. 3% are also leu+ and
0% are also aziR.
• By this we can see that thr is closer to leu than it is to
azi, because thr and azi are so far apart that they are
never co-transduced.
• Thus the order must be thr--leu--azi.
• Note that the co-transduction frequency for thr and
leu are slightly different for the 2 experiments: 2%
and 3%. This is attributable to experimental error.
31
Intro to Specialized Transduction
• Some phages can transfer only particular genes to
other bacteria.
• Phage lambda (λ) has this property. To understand
specialized transduction, we need to examine the
phage lambda life cycle.
• lambda has 2 distinct phases of its life cycle. The
“lytic” phase is the same as we saw with the general
phage life cycle: the phage infects the cell, makes
more copies of itself, then lyses the cell to release
the new phage.
32
Lysogenic Phase
• The “lysogenic” phase of the lambda life cycle starts the same way: the
lambda phage binds to the bacterial cell and injects its DNA. Once
inside the cell, the lambda DNA circularizes, then incorporates into the
bacterial chromosome by a crossover, similar to the conversion of an F
plasmid into an Hfr.
• Once incorporated into the chromosome, the lambda DNA becomes
quiescent: its genes are not expressed and it remains a passive
element on the chromosome, being replicated along with the rest of
the chromosome. The lambda DNA in this condition is called the
“prophage”.
• After many generations of the cell, conditions might get harsh. For
lambda, bad conditions are signaled when DNA damage occurs.
• When the lambda prophage receives the DNA damage signal, it loops
out and has a crossover, removing itself from the chromosome. Then
the lambda genes become active and it goes into the lytic phase,
reproducing itself, then lysing the cell.
33
Specialized Transduction
• Unlike the F plasmid that can incorporate anywhere in the E. coli genome,
lambda can only incorporate into a specific site, called attλ. The gal gene
is on one side of attλ and the bio gene (biotin synthesis) is on the other
side.
• Sometimes when lambda come out of the chromosome at the end of the
lysogenic phase, it crosses over at the wrong point. This is very similar to
the production of an F’ from an Hfr.
• When this happens, a piece of the E. coli chromosome is incorporated into
the lambda phage chromosome
• These phage that carry an E. coli gene in addition to the lambda genes are
called “specialized transducing phages”. They can carry either the gal gene
or the bio gene to other E. coli.
• Thus it is possible to quickly develop merodiploids (partial diploids) for any
allele you like of gal or bio. Note that this trick can’t be used with other
genes, but only for genes that flank the attachment site for lambda or
another lysogenic phage.
34
Specialized Transduction
35
5
POPULATION GENETICS:
The study of the rules governing the
maintenance and transmission of genetic
variation in natural populations.
DARWINIAN EVOLUTION BY NATURAL SELECTION
 Many more individuals are born than survive (COMPETITION).
 Individuals within species are variable (VARIATION).
 Some of these variations are passed on to offspring (HERITABILITY).
 Survival and reproduction are not random. There must be a correlation between
fitness and phenotype.
Gregor Mendel
The “rediscovery” of Mendel’s genetic studies in 1902
by William Bateson completed the missing model for
the inheritance of genetic factors.
 Mendel published his work in the Transactions of
the Brunn Society of Natural History in 1866.
SEXUAL REPRODUCTION CONTRIBUTES TO VARIATION
Example – A Line Cross Experiment
Consider 2 diploid individuals with 3 loci and 2 alleles,
Parents: aabbcc x AABBCC
F1 progeny: AaBbCc
F2 progeny:
AABBCC AABBCc AABBcc
AABbCC AABbCc AABbcc
AAbbCC AAbbCc AAbbcc
AaBBCC AaBBCc AaBBcc
AaBbCC AaBbCc AaBbcc
AabbCC AabbCc Aabbcc
aaBBCC aaBBCc aaBBcc
aaBbCC aaBbCc aaBbcc
aabbCC aabbCc aabbcc
27
COMBINIATIONS
Mechanisms of Evolution: Mendelian Genetics in
Populations
 Genetic variation is the raw material of evolutionary change: how do we measure it?
 What are the forces that cause genetic changes within populations? That is, what
mechanisms cause evolutionary change?
Population Genetics
 Evolution can be defined as a change in gene frequencies through time.
 Population genetics tracks the fate, across generations, of Mendelian genes in
populations.
 Population genetics is concerned with whether a particular allele or genotype will
become more or less common over time, and WHY.
A few things to keep in mind as we take an
excursion into population genetic theory:
“Make things as simple as possible, but no simpler.”
---Einstein
“All models are wrong, some are useful.”
---Box
“No theory should fit all the facts because some of the facts are wrong.”
---Bohr
Some Definitions:
 Population: A freely interbreeding group of individuals.
 Gene Pool: The sum total of genetic information present in a population at
any given point in time.
 Phenotype: A morphological, physiological, biochemical, or behavioral
characteristic of an individual organism.
 Genotype: The genetic constitution of an individual organism.
 Locus: A site on a chromosome, or the gene that occupies the site.
 Gene: A nucleic acid sequence that encodes a product with a distinct
function in the organism.
 Allele: A particular form of a gene.
 Gene (Allele) Frequency: The relative proportion of a particular allele at a
single locus in a population (a number between 0 and 1).
 Genotype Frequency: The relative proportion of a particular genotype in a
population (a number between 0 and 1).
The Gene Pool
•Members of a species can
interbreed & produce fertile
offspring
•Species have a shared gene
pool
•Gene pool – all of the alleles
of all individuals in a
population
44
2
The Gene Pool
•Different species do
NOT exchange genes by
interbreeding
•Different species that
interbreed often
produce sterile or less
viable offspring e.g.
Mule
45
Assumptions:
1) Diploid, autosomal locus with 2 alleles: A and a
2) Simple life cycle:
PARENTS GAMETES ZYGOTES
(DIPLIOD) (HAPLOID) (DIPLOID)
These parents produce a large gamete pool (Gene Pool) containing alleles A and
a.
a A A a
a A A a A a a
a A A a a A a A A
a a A A a a a
a A a a A A
A a A
Gamete (allele) Frequencies:
Freq(A) = p
Freq(a) = q
 p + q = 1
Genotype Frequencies of 3 Possible Zygotes:
AA Aa aa
Freq (AA) = pA x pA = pA
2
Freq (Aa) = (pA x qa) + (qa x pA) = 2pAqa
Freq (aa) = qa x qa = qa
2
 p2 + 2pq + q2 = 1
General Rule for Estimating Allele Frequencies from
Genotype 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)
Sample Calculation: Allele Frequencies
Assume N = 200 indiv. in each of two populations 1 & 2
 Pop 1 : 90 AA 40 Aa 70 aa
 Pop 2 : 45 AA 130 Aa 25 aa
In Pop 1 :
 p = p2 + ½ (2pq) = 90/200 + ½ (40/200) = 0.45 + 0.10 = 0.55
 q = q2 + ½ (2pq) = 70/200 + ½ (40/200) = 0.35 + 0.10 = 0.45
In Pop 2 :
 p = p2 + ½ (2pq) = 45/200 + ½ (130/200) = 0.225 + 0.325 = 0.55
 q = q2 + ½ (2pq) = 25/200 + ½ (130/200) = 0.125 + 0.325 = 0.45
Main Points:
 p + q = 1 (more generally, the sum of the allele
frequencies equals one)
 p2 + 2pq +q2 = 1 (more generally, the sum of the
genotype frequencies equals one)
 Two populations with markedly different genotype
frequencies can have the same allele frequencies
Populations
•A group of the same
species living in an area
•No two individuals are
exactly alike (variations)
•More Fit individuals
survive & pass on their
traits
51
Speciation
•Formation of new
species
•One species may split
into 2 or more species
•A species may evolve
into a new species
•Requires very long
periods of time
52
Modern Evolutionary Thought
Modern Synthesis Theory
 Combines Darwinian
selection and Mendelian
inheritance
 Population genetics - study
of genetic variation within
a population
 Emphasis on quantitative
characters (height, size …)
54
Modern Synthesis Theory
 1940s – comprehensive theory
of evolution (Modern Synthesis
Theory)
 Introduced by Fisher & Wright
 Until then, many did not
accept that Darwin’s theory of
natural selection could drive
evolution
55
S. Wright
A. Fisher
Modern Synthesis Theory
• TODAY’S theory on evolution
 Recognizes that GENES are responsible for the
inheritance of characteristics
 Recognizes that POPULATIONS, not individuals, evolve
due to natural selection & genetic drift
 Recognizes that SPECIATION usually is due to the
gradual accumulation of small genetic changes
56
Microevolution
• Changes occur in gene pools due to mutation,
natural selection, genetic drift, etc.
• Gene pool changes cause more VARIATION in
individuals in the population
• This process is called MICROEVOLUTION
• Example: Bacteria becoming unaffected by
antibiotics (resistant)
57
Hardy-Weinberg Principle
The Hardy-Castle-Weinberg Law
 A single generation of random mating establishes
H-W equilibrium genotype frequencies, and neither
these frequencies nor the gene frequencies will
change in subsequent generations.
Hardy
p2 + 2pq + q2 = 1
The Hardy-Weinberg Principle
• Used to describe a non-evolving population.
• Shuffling of alleles by meiosis and random
fertilization have no effect on the overall
gene pool.
• Natural populations are NOT expected to
actually be in Hardy-Weinberg equilibrium.
60
The Hardy-Weinberg Principle
• Deviation from Hardy-Weinberg equilibrium
usually results in evolution
• Understanding a non-evolving population,
helps us to understand how evolution occurs
61
5 Assumptions of the H-W Principle
1. Large population size
- small populations have fluctuations in allele
frequencies (e.g., fire, storm).
2. No migration
- immigrants can change the frequency of an allele by
bringing in new alleles to a population.
3. No net mutations
- if alleles change from one to another, this will change
the frequency of those alleles
62
5 Assumptions of the H-W Principle
4. Random mating
- if certain traits are more desirable, then individuals
with those traits will be selected and this will not
allow for random mixing of alleles.
5. No natural selection
- if some individuals survive and reproduce at a
higher rate than others, then their offspring will carry
those genes and the frequency will change for the
next generation.
63
The Hardy-Weinberg Principle
The gene pool of a NON-EVOLVING population remains
CONSTANT over multiple generations (allele
frequency doesn’t change)
The Hardy-Weinberg Equation:
1.0 = p2 + 2pq + q2
Where:
p2 = frequency of AA genotype
2pq = frequency of Aa
q2 = frequency of aa genotype
64
The Hardy-Weinberg Principle
Determining the Allele Frequency using Hardy-
Weinberg:
1.0 = p + q
Where:
p = frequency of A allele
q = frequency of a allele
65
66
Allele Frequencies Define Gene Pools
As there are 1000 copies of the genes for color,
the allele frequencies are (in both males and females):
320 x 2 (RR) + 160 x 1 (Rr) = 800 R; 800/1000 = 0.8 (80%) R
160 x 1 (Rr) + 20 x 2 (rr) = 200 r; 200/1000 = 0.2 (20%) r
500 flowering plants
480 red flowers 20 white flowers
320 RR 160 Rr 20 rr
IMPLICATIONS OF THE H-W PRINCIPLE:
1) A random mating population with no external forces acting on it will reach the
equilibrium H-W frequencies 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.
2pq has a maximum value of 0.5 when
p = q = 0.5
FOUR PRIMARY USES OF THE H-W 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.
References
• Images references:
• 1-6- Gene cloning and DNA analysis by TA Brown
• Reading references:
• Gene cloning and DNA analysis by TA Brown
1

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Gene mapping and microbial genetics techniques

  • 1. Linkage, crossing over and basic microbial genetics Cell biology and Genetics Unit – 5
  • 2. Mapping of gene • Genome mapping, is the creation of a genetic map assigning DNA fragments to chromosomes. • Genetic linkage is the tendency of alleles that are located close together on a chromosome to be inherited together during meiosis. Genes whose loci are nearer to each other are less likely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be genetically linked. In other words, the nearer two genes are on a chromosome, the lower is the chance of a swap occurring between them, and the more likely they are to be inherited together.
  • 3. Linkage map • A linkage map is a genetic map of a species or experimental population that shows the position of its known genes or genetic markers relative to each other in terms of recombination frequency, rather than a specific physical distance along each chromosome. • Linkage mapping is critical for identifying the location of genes that cause genetic diseases. • A genetic map is a map based on the frequencies of recombination between markers during crossover of homologous chromosomes.
  • 4. • The greater the frequency of recombination (segregation) between two genetic markers, the further apart they are assumed to be. Conversely, the lower the frequency of recombination between the markers, the smaller the physical distance between them. • Historically, the markers originally used were detectable phenotypes (enzyme production, eye color) derived from coding DNA sequences; eventually, confirmed or assumed non coding DNA sequences such as microsatellites or those generating restriction fragment length polymorphisms (RFLPs) have been used. • Genetic maps help researchers to locate other markers, such as other genes by testing for genetic linkage of the already known markers. • A genetic map is not a physical map (such as a radiation reduced hybrid map) or gene map.
  • 5. Genome sequencing • Genome sequencing are sometimes mistakenly referred to as "genome mapping" by non-biologists. While the scope, purpose and process are totally different, a genome assembly can be viewed as the "ultimate" form of physical map, in that it provides all information that a traditional physical map can offer in a much better way.
  • 6. Gene mapping • The essence of all genome mapping is to place a collection of molecular markers onto their respective positions on the genome. • Molecular markers come in all forms. Genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers. • In genetic mapping, any sequence feature that can be faithfully distinguished from the two parents can be used as a genetic marker. Genes, in this regard, are represented by "traits" that can be faithfully distinguished between two parents. • In physical mapping, there are no direct ways of marking up a specific gene since the mapping do not include any information that concern traits and functions. Genetic markers can be linked to a physical map by processes in situ hybridization. By this approach, physical map contigs can be "anchored" onto a genetic map.
  • 7. Physical Mapping • In physical mapping, the DNA is cut by a restriction enzyme. Once cut, the DNA fragments are separated by electrophoresis. The resulting pattern of DNA migration (i.e., its genetic fingerprint) is used to identify what stretch of DNA is in the clone. By analyzing the fingerprints, contigs are assembled by automated (FPC) or manual means (Pathfinders) into overlapping DNA stretches. Now a good choice of clones can be made to efficiently sequence the clones to determine the DNA sequence of the organism under study (seed picking). • Macrorestriction is a type of physical mapping wherein the high molecular weight DNA is digested with a restriction enzyme having a low number of restriction sites. • There are alternative ways to determine how DNA in a group of clones overlap without completely sequencing the clones. Once the map is determined, the clones can be used as a resource to efficiently contain large stretches of the genome. This type of mapping is more accurate than genetic maps.
  • 8. Recombination • The exchange of DNA sequences between different molecules, occurring either naturally or as a result of DNA manipulation. • A process by which pieces of DNA are broken and recombined to produce new combinations of alleles.
  • 9. What is gene cloning? 1 A fragment of DNA, containing the gene to be cloned, is inserted into a circular DNA molecule called a vector, to produce a recombinant DNA molecule. 2 The vector transports the gene into a host cell, which is usually a bacterium, although other types of living cell can be used. 3 Within the host cell the vector multiplies, producing numerous identical copies, not only of itself but also of the gene that it carries.
  • 10. 4 When the host cell divides, copies of the recombinant DNA molecule are passed to the progeny and further vector replication takes place. 5 After a large number of cell divisions, a colony, or clone, of identical host cells is produced. Each cell in the clone contains one or more copies of the recombinant DNA molecule; the gene carried by the recombinant molecule is now said to be cloned.
  • 11. 1
  • 12. Crossing Over • (i) Crossing over is a recombination of genes due to exchange of genetic material between two homologous chromosomes, • (ii) It is the mutual exchange of segments of genetic material between non-sister chromatids of two homologous chromosomes, so as to produce re- combinations or new combinations of genes. • The non-sister chromatids in which exchange of segments have occurred are called recombinants or cross-overs while the other chromatids in which crossing over has not taken place are known as parental chromatids or non cross-overs.
  • 13. • Each parent cell has pairs of homologous chromosomes, one homolog from the father and one from the mother. In meiosis, the maternal and paternal chromosomes can be shuffled into the daughter cells in many different combinations (in humans there are 223 possible combinations!).
  • 14. • This ensures genetic variation in sexually reproducing organisms. Further genetic variation comes from crossing over, which may occur during prophase I of meiosis. • In prophase I of meiosis, the replicated homologous pair of chromosomes comes together in the process called synapsis, and sections of the chromosomes are exchanged. You can see that after crossing over, the resultant chromosomes are neither entirely maternal nor entirely paternal, but contain genes from both parents. Synapsis and crossing over occur only in meiosis.
  • 15. Bacterial Sexual Processes • Eukaryotes have the processes of meiosis to reduce diploids to haploidy, and fertilization to return the cells to the diploid state. Bacterial sexual processes are not so regular. However, they serve the same aim: to mix the genes from two different organisms together. • The three bacterial sexual processes: – 1. conjugation: direct transfer of DNA from one bacterial cell to another. – 2. transduction: use of a bacteriophage (bacterial virus) to transfer DNA between cells. – 3. transformation: naked DNA is taken up from the environment by bacterial cells. 15
  • 16. Transformation • The essence of recombinant DNA technology is to remove DNA from cells, manipulate it in the test tube, then put it back into living cells. In most cases this is done by transformation. • In the case of E. coli, cells are made “competent” to be transformed by treatment with calcium ions and heat shock. E. coli cells in this condition readily pick up DNA from their surroundings and incorporate it into their genomes. 16 2
  • 17. Gene Transfer by Transformation •Transformation is the process of importing free DNA into bacterial cells. • the cells need to be competent. • Many cells are capable of natural Transformation and naturally competent. • others require artificial manipulations. • Perturbing the membrane by chemical (CaCl2) or electrical (electroporation) methods • Not all bacteria can take up free or naked DNA (<1%). 17
  • 18. Gram positive Bacteria transform DNA using a Transformasome complex Gram-negative bacteria do not use transformasomes 18 3
  • 19. Conjugation • Physical contact between two bacteria, usually associated with transfer of DNA from one cell to the other.
  • 20. Conjugation • Conjugation is the closest analogue in bacteria to eukaryotic sex. • The ability to conjugate is conferred by the F plasmid. A plasmid is a small circle of DNA that replicates independently of the chromosome. Bacterial cells that contain an F plasmid are called “F+”. Bacteria that don’t have an F plasmid are called “F-”. • F+ cells grow special tubes called “sex pilli” from their bodies. When an F+ cell bumps into an F- cell, the sex pilli hold them together, and a copy of the F plasmid is transferred from the F+ to the F-. Now both cells are F+. 20
  • 21. 21 4
  • 22. Hfr Conjugation • When it exists as a free plasmid, the F plasmid can only transfer itself. This isn’t all that useful for genetics. • However, sometimes the F plasmid can become incorporated into the bacterial chromosome, by a crossover between the F plasmid and the chromosome. The resulting bacterial cell is called an “Hfr”, which stands for “High frequency of recombination”. • Hfr bacteria conjugate just like F+ do, but they drag a copy of the entire chromosome into the F- cell. • Technique used in bacterial gene mapping 22
  • 23. Intracellular Events in Conjugation • The piece of chromosome that enters the F- form the Hfr is linear. It is called the “exogenote”. • The F- cell’s own chromosome is circular. It is called the “endogenote”. • Only circular DNA replicates in bacteria, so genes on the exogenote must be transferred to the endogenote for the F- to propagate them. • This is done by recombination: 2 crossovers between homologous regions of the exogenote and the endogenote. In the absence of recombination, conjugation in ineffective: the exogenote enters the F-, but all the genes on it are lost as the bacterial cell reproduces. 23
  • 24. F-prime (F’) • The process of making an Hfr from an F+ involves a crossover between the F plasmid and the chromosome. This process is reversible: an Hfr can revert to being F+ when the F plasmid DNA incorporated into the Hfr chromosome has a crossover and loops out of the chromosome forming an F plasmid once again. • Sometimes the looping-out and crossing-over process doesn’t happen at the proper place. When this happens, a piece of the bacterial chromosome can become incorporated into the F plasmid. This is called an F’ (F-prime) plasmid. • F’ plasmids can be transferred by conjugation. Conjugation with an F’ (or a regular F plasmid) is much faster and more efficient than with an Hfr, because only a very small piece of DNA is transferred. Since the F’ carries a bacterial gene, this allele can be rapidly moved into a large number of other strains. This permits its function to be tested rapidly. Also, tests of dominance can be done. • A cell containing an F’ is “merodiploid”: part diploid and part haploid. It is diploid for the bacterial gene carried by the F’ (one copy on the F’ and the other on the chromosome), and haploid for all other genes. 24
  • 25. Transduction • Transduction is the process of moving bacterial DNA from one cell to another using a bacteriophage. • Bacteriophage or just “phage” are bacterial viruses. They consist of a small piece of DNA inside a protein coat. The protein coat binds to the bacterial surface, then injects the phage DNA. The phage DNA then takes over the cell’s machinery and replicates many virus particles. • Two forms of transduction: – 1. generalized: any piece of the bacterial genome can be transferred – 2. specialized: only specific pieces of the chromosome can be transferred. 25
  • 26. General Phage Life Cycle • 1. Phage attaches to the cell and injects its DNA. • 2. Phage DNA replicates, and is transcribed into RNA, then translated into new phage proteins. • 3. New phage particles are assembled. • 4. Cell is lysed, releasing about 200 new phage particles. • Total time = about 15 minutes. 26
  • 28. Generalized Transduction • Some phages, such as phage P1, break up the bacterial chromosome into small pieces, and then package it into some phage particles instead of their own DNA. • These chromosomal pieces are quite small. • A phage containing E. coli DNA can infect a fresh host, because the binding to the cell surface and injection of DNA is caused by the phage proteins. • After infection by such a phage, the cell contains an exogenote (linear DNA injected by the phage) and an endogenote (circular DNA that is the host’s chromosome). • A double crossover event puts the exogenote’s genes onto the chromosome, allowing them to be propagated. 28
  • 29. Transduction Mapping • Only a small amount of chromosome, a few genes, can be transferred by transduction. The closer 2 genes are to each other, the more likely they are to be transduced by the same phage. Thus, “co- transduction frequency” is the key parameter used in mapping genes by transduction. • Transduction mapping is for fine-scale mapping only. Conjugation mapping is used for mapping the major features of the entire chromosome. 29
  • 30. Mapping Experiment • Important point: the closer 2 genes are to each other, the higher the co-transduction frequency. • We are just trying to get the order of the genes here, not put actual distances on the map. • Expt: donor strain is aziR leu+ thr+. Phage P1 is grown on the donor strain, and then the resulting phage are mixed with the recipient strain: aziS leu- thr-. The bacteria that survive are then tested for various markers • 1. Of the leu+ cells, 50% are aziR, and 2% are thr+. From this we can conclude that azi and leu are near each other, and that leu and thr are far apart. • But: what is the order: leu--azi--thr, or azi--leu--thr ? 30
  • 31. Mapping Experiment, pt. 2 • 2. Do a second experiment to determine the order. Select the thr+ cells, then determine how many of them have the other 2 markers. 3% are also leu+ and 0% are also aziR. • By this we can see that thr is closer to leu than it is to azi, because thr and azi are so far apart that they are never co-transduced. • Thus the order must be thr--leu--azi. • Note that the co-transduction frequency for thr and leu are slightly different for the 2 experiments: 2% and 3%. This is attributable to experimental error. 31
  • 32. Intro to Specialized Transduction • Some phages can transfer only particular genes to other bacteria. • Phage lambda (λ) has this property. To understand specialized transduction, we need to examine the phage lambda life cycle. • lambda has 2 distinct phases of its life cycle. The “lytic” phase is the same as we saw with the general phage life cycle: the phage infects the cell, makes more copies of itself, then lyses the cell to release the new phage. 32
  • 33. Lysogenic Phase • The “lysogenic” phase of the lambda life cycle starts the same way: the lambda phage binds to the bacterial cell and injects its DNA. Once inside the cell, the lambda DNA circularizes, then incorporates into the bacterial chromosome by a crossover, similar to the conversion of an F plasmid into an Hfr. • Once incorporated into the chromosome, the lambda DNA becomes quiescent: its genes are not expressed and it remains a passive element on the chromosome, being replicated along with the rest of the chromosome. The lambda DNA in this condition is called the “prophage”. • After many generations of the cell, conditions might get harsh. For lambda, bad conditions are signaled when DNA damage occurs. • When the lambda prophage receives the DNA damage signal, it loops out and has a crossover, removing itself from the chromosome. Then the lambda genes become active and it goes into the lytic phase, reproducing itself, then lysing the cell. 33
  • 34. Specialized Transduction • Unlike the F plasmid that can incorporate anywhere in the E. coli genome, lambda can only incorporate into a specific site, called attλ. The gal gene is on one side of attλ and the bio gene (biotin synthesis) is on the other side. • Sometimes when lambda come out of the chromosome at the end of the lysogenic phase, it crosses over at the wrong point. This is very similar to the production of an F’ from an Hfr. • When this happens, a piece of the E. coli chromosome is incorporated into the lambda phage chromosome • These phage that carry an E. coli gene in addition to the lambda genes are called “specialized transducing phages”. They can carry either the gal gene or the bio gene to other E. coli. • Thus it is possible to quickly develop merodiploids (partial diploids) for any allele you like of gal or bio. Note that this trick can’t be used with other genes, but only for genes that flank the attachment site for lambda or another lysogenic phage. 34
  • 36. POPULATION GENETICS: The study of the rules governing the maintenance and transmission of genetic variation in natural populations.
  • 37. DARWINIAN EVOLUTION BY NATURAL SELECTION  Many more individuals are born than survive (COMPETITION).  Individuals within species are variable (VARIATION).  Some of these variations are passed on to offspring (HERITABILITY).  Survival and reproduction are not random. There must be a correlation between fitness and phenotype.
  • 38. Gregor Mendel The “rediscovery” of Mendel’s genetic studies in 1902 by William Bateson completed the missing model for the inheritance of genetic factors.  Mendel published his work in the Transactions of the Brunn Society of Natural History in 1866.
  • 39. SEXUAL REPRODUCTION CONTRIBUTES TO VARIATION Example – A Line Cross Experiment Consider 2 diploid individuals with 3 loci and 2 alleles, Parents: aabbcc x AABBCC F1 progeny: AaBbCc F2 progeny: AABBCC AABBCc AABBcc AABbCC AABbCc AABbcc AAbbCC AAbbCc AAbbcc AaBBCC AaBBCc AaBBcc AaBbCC AaBbCc AaBbcc AabbCC AabbCc Aabbcc aaBBCC aaBBCc aaBBcc aaBbCC aaBbCc aaBbcc aabbCC aabbCc aabbcc 27 COMBINIATIONS
  • 40. Mechanisms of Evolution: Mendelian Genetics in Populations  Genetic variation is the raw material of evolutionary change: how do we measure it?  What are the forces that cause genetic changes within populations? That is, what mechanisms cause evolutionary change?
  • 41. Population Genetics  Evolution can be defined as a change in gene frequencies through time.  Population genetics tracks the fate, across generations, of Mendelian genes in populations.  Population genetics is concerned with whether a particular allele or genotype will become more or less common over time, and WHY.
  • 42. A few things to keep in mind as we take an excursion into population genetic theory: “Make things as simple as possible, but no simpler.” ---Einstein “All models are wrong, some are useful.” ---Box “No theory should fit all the facts because some of the facts are wrong.” ---Bohr
  • 43. Some Definitions:  Population: A freely interbreeding group of individuals.  Gene Pool: The sum total of genetic information present in a population at any given point in time.  Phenotype: A morphological, physiological, biochemical, or behavioral characteristic of an individual organism.  Genotype: The genetic constitution of an individual organism.  Locus: A site on a chromosome, or the gene that occupies the site.  Gene: A nucleic acid sequence that encodes a product with a distinct function in the organism.  Allele: A particular form of a gene.  Gene (Allele) Frequency: The relative proportion of a particular allele at a single locus in a population (a number between 0 and 1).  Genotype Frequency: The relative proportion of a particular genotype in a population (a number between 0 and 1).
  • 44. The Gene Pool •Members of a species can interbreed & produce fertile offspring •Species have a shared gene pool •Gene pool – all of the alleles of all individuals in a population 44 2
  • 45. The Gene Pool •Different species do NOT exchange genes by interbreeding •Different species that interbreed often produce sterile or less viable offspring e.g. Mule 45
  • 46. Assumptions: 1) Diploid, autosomal locus with 2 alleles: A and a 2) Simple life cycle: PARENTS GAMETES ZYGOTES (DIPLIOD) (HAPLOID) (DIPLOID) These parents produce a large gamete pool (Gene Pool) containing alleles A and a. a A A a a A A a A a a a A A a a A a A A a a A A a a a a A a a A A A a A
  • 47. Gamete (allele) Frequencies: Freq(A) = p Freq(a) = q  p + q = 1 Genotype Frequencies of 3 Possible Zygotes: AA Aa aa Freq (AA) = pA x pA = pA 2 Freq (Aa) = (pA x qa) + (qa x pA) = 2pAqa Freq (aa) = qa x qa = qa 2  p2 + 2pq + q2 = 1
  • 48. General Rule for Estimating Allele Frequencies from Genotype 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)
  • 49. Sample Calculation: Allele Frequencies Assume N = 200 indiv. in each of two populations 1 & 2  Pop 1 : 90 AA 40 Aa 70 aa  Pop 2 : 45 AA 130 Aa 25 aa In Pop 1 :  p = p2 + ½ (2pq) = 90/200 + ½ (40/200) = 0.45 + 0.10 = 0.55  q = q2 + ½ (2pq) = 70/200 + ½ (40/200) = 0.35 + 0.10 = 0.45 In Pop 2 :  p = p2 + ½ (2pq) = 45/200 + ½ (130/200) = 0.225 + 0.325 = 0.55  q = q2 + ½ (2pq) = 25/200 + ½ (130/200) = 0.125 + 0.325 = 0.45
  • 50. Main Points:  p + q = 1 (more generally, the sum of the allele frequencies equals one)  p2 + 2pq +q2 = 1 (more generally, the sum of the genotype frequencies equals one)  Two populations with markedly different genotype frequencies can have the same allele frequencies
  • 51. Populations •A group of the same species living in an area •No two individuals are exactly alike (variations) •More Fit individuals survive & pass on their traits 51
  • 52. Speciation •Formation of new species •One species may split into 2 or more species •A species may evolve into a new species •Requires very long periods of time 52
  • 54. Modern Synthesis Theory  Combines Darwinian selection and Mendelian inheritance  Population genetics - study of genetic variation within a population  Emphasis on quantitative characters (height, size …) 54
  • 55. Modern Synthesis Theory  1940s – comprehensive theory of evolution (Modern Synthesis Theory)  Introduced by Fisher & Wright  Until then, many did not accept that Darwin’s theory of natural selection could drive evolution 55 S. Wright A. Fisher
  • 56. Modern Synthesis Theory • TODAY’S theory on evolution  Recognizes that GENES are responsible for the inheritance of characteristics  Recognizes that POPULATIONS, not individuals, evolve due to natural selection & genetic drift  Recognizes that SPECIATION usually is due to the gradual accumulation of small genetic changes 56
  • 57. Microevolution • Changes occur in gene pools due to mutation, natural selection, genetic drift, etc. • Gene pool changes cause more VARIATION in individuals in the population • This process is called MICROEVOLUTION • Example: Bacteria becoming unaffected by antibiotics (resistant) 57
  • 59. The Hardy-Castle-Weinberg Law  A single generation of random mating establishes H-W equilibrium genotype frequencies, and neither these frequencies nor the gene frequencies will change in subsequent generations. Hardy p2 + 2pq + q2 = 1
  • 60. The Hardy-Weinberg Principle • Used to describe a non-evolving population. • Shuffling of alleles by meiosis and random fertilization have no effect on the overall gene pool. • Natural populations are NOT expected to actually be in Hardy-Weinberg equilibrium. 60
  • 61. The Hardy-Weinberg Principle • Deviation from Hardy-Weinberg equilibrium usually results in evolution • Understanding a non-evolving population, helps us to understand how evolution occurs 61
  • 62. 5 Assumptions of the H-W Principle 1. Large population size - small populations have fluctuations in allele frequencies (e.g., fire, storm). 2. No migration - immigrants can change the frequency of an allele by bringing in new alleles to a population. 3. No net mutations - if alleles change from one to another, this will change the frequency of those alleles 62
  • 63. 5 Assumptions of the H-W Principle 4. Random mating - if certain traits are more desirable, then individuals with those traits will be selected and this will not allow for random mixing of alleles. 5. No natural selection - if some individuals survive and reproduce at a higher rate than others, then their offspring will carry those genes and the frequency will change for the next generation. 63
  • 64. The Hardy-Weinberg Principle The gene pool of a NON-EVOLVING population remains CONSTANT over multiple generations (allele frequency doesn’t change) The Hardy-Weinberg Equation: 1.0 = p2 + 2pq + q2 Where: p2 = frequency of AA genotype 2pq = frequency of Aa q2 = frequency of aa genotype 64
  • 65. The Hardy-Weinberg Principle Determining the Allele Frequency using Hardy- Weinberg: 1.0 = p + q Where: p = frequency of A allele q = frequency of a allele 65
  • 66. 66 Allele Frequencies Define Gene Pools As there are 1000 copies of the genes for color, the allele frequencies are (in both males and females): 320 x 2 (RR) + 160 x 1 (Rr) = 800 R; 800/1000 = 0.8 (80%) R 160 x 1 (Rr) + 20 x 2 (rr) = 200 r; 200/1000 = 0.2 (20%) r 500 flowering plants 480 red flowers 20 white flowers 320 RR 160 Rr 20 rr
  • 67. IMPLICATIONS OF THE H-W PRINCIPLE: 1) A random mating population with no external forces acting on it will reach the equilibrium H-W frequencies 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. 2pq has a maximum value of 0.5 when p = q = 0.5
  • 68. FOUR PRIMARY USES OF THE H-W 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.
  • 69. References • Images references: • 1-6- Gene cloning and DNA analysis by TA Brown • Reading references: • Gene cloning and DNA analysis by TA Brown 1