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COMPARATIVE GENOMICS
II
Variation in Chromosome Structure
GENE 330
Genetic Variation in Natural Pop. Cont...
• Without variation, populations evolve. Soon after Mendel’s principles were
rediscovered, biologists began to document genetic variation in natural population
• Initially, these efforts focused on conspicuous features of the phenotypepigmentation, size and so forth. Later, they emphasized characteristics that are
more directly related to chromosomes and genes
VARIATION IN PHENOTYPES
• There are phenotypic variation within many species, e.g., land snails have
different colored bands on their shells, squirrels and other small mammals have
different patterns
• In plant kingdom, phenotypic variation maybe manifested by different kinds of
flowers
• All these phenotypic differences may have a genetic basis. However, to evaluate the
underlying genetic factors, it is necessary to bring the organisms into the laboratory
and cross them with others.
• Unfortunately, for many species this approach is not feasible. Thus, geneticists
have tendered to focus their investigations of naturally occurring phenotypic
variation on organisms that can be reared and bred in the laboratory
Yellow Tiger Swallowtail
(Papilio glaucuas)
Black Tiger Swallowtail
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
• Phenotypic variation can be reflection of the underlying genetic
variability
• The four common types of chromosomal mutations leading to changes in
structure are:
deletions, duplications, inversions and translocations.
All result from breaks in chromosomes
• Flies captured in the wild can be captured in the laboratory and bred to
produce larvae, which can be examined for alterations in the banding
patterns of their polytene chromosomes
KARYOTYPING: THE BEGINNING OF
COMPARATIVE GENETICS
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The term “karyotype” refers to a description or depiction (karyogram) of
the set of all chromosomes in organism. It is customary to depict the
autosomal (nonsex) chromosomes arranged in homologous pairs in a
standard order, usually from largest to smallest, with the shorter arm of
each one oriented toward the top of the picture.
The sex chromosomes typically are placed last.
Each eukaryotic chromosome is linear with a constriction somewhere
along its length called the centromere, and is capped by condensed
regions called telomeres.
Each chromosome looks more like the letter X, with each arm in two
replicates (sister chromatids) emanating from the centromere.
The shorter arm is designated as the “p” arm (petit- little); the longer
arm is labeled the “q” arm (queue-tail).
KARYOTYPING: THE BEGINNING OF
COMPARATIVE GENOMICS
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Different banding techniques provide cytogeneticists with the means to
analyze fine details of chromosome structure.
Until the late 1960s and early 1970s, chromosome spreads were stained
with Feulgen’s reagent.
More detailed studies now employ dyes that stain chromosomes differentially
along their lengths. Several types of banding can be produced by different
dyes and treatments.
Chromosomes they have been stained with quinacrine or giemsa create a
reproducible pattern of bands on each chromosome.
Today are used a different staining procedures called ;
- Q banding (Quinacrine stain)
- G banding (Gienmsa stain)
- R banding (reverse patterns-dark bands that corresponds to light G
bands)
- C banding (stain the region around centromere)
Using these bands, cytogeneticists can identify particular chromosomes in a
cell, and they can analyze these chromosomes for structural abnormalities.
KARYOTYPING: THE BEGINNING OF COMPARATIVE
GENOMICS
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The correct chromosome count for humans was not established until
1956.
A great deal of variation among karyotypes of different organisms was
apparent.
In some organisms, the chromosomes all have the same morphology
(e.g. all mouse chromosomes are acrocentric- centromere near the end),
other organisms, such as humans, have a mixture of different
chromosome morphological types.
Chromosomes vary considerably in size and numbers of chromosomes.
Even closely related and phenotypically similar species can differ greatly
in chromosome number.
Preparation of cells for cytological analysis.
Q bands – the band appear only when the chromosomes are exposed to UV light.
G banding
Polytene chromosomes are a giant chromosome containing nonseparated multiple copies of replicated DNA
Polytene chromosomes in Drosophila
Banding pattern of the polytene X chromosome. Chromosome is divided
into 20 numbered sections.
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
• D. pseudoobscura and D. persimilis are subling species – morphologically similar
and able to be interbred in the laboratory. However, hybrid males from these crosses
are sterile and hybrid females have severely reduced fertility.
• D. mirand is less closely related to other two species. It rarely produce hybrids in
crosses with neither D. pseudoobscura nor D. persimilis, and when hybrids are
produces, they are always sterile
• There are many different arrangements of the banding patterns in the polytene
chromosomes of the species
• Each arrangement consists of one or more inversions of the most common banding
pattern. e.g. in the third chromosome of D. pseudoobscura, there 17 different
arrangements in natural population
• The standard banding pattern (ST) is most frequent in populations along the coast of
California (48%) and in Northern Mexico (58%)
• Different arrangements predominates in other areas, e.g., 88% Arrowhead (AR)
arrangement in Arizon, Nevad and Atah. 71% Pike’s Peak (PP) arrangement in Taxas
• The changes in arrangement frequencies are both seasonally and long-term
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
•Chromosomes can undergo several types of changes which fall into two classes. The
first type of change involves changes in chromosome number and is referred to as
aneuploidy and euploidy
• The chromosomal changes alter the linear order of the chromosome and occur
because of deletions, duplications, inversions, translocations and insertions of
chromosomal DNA
• The analysis of these types of changes to a large part has been performed in genetic
stocks of the fruit fly, Drosophila melanogaster
• The chromosomes of this species are of particular interest, are those found in the
salivary glands of larvae
• These tissues grow not by cell division but by enlargement. During this enlargement
the chromosomes also undergo replication but this replication is different than in other
tissues because:
1. the homologous chromosomes remain synapsed, that is paired throughout the
duplication; and
2. the chromosomes undergo about ten rounds of replication to produce 1210 (1024)
double-stranded DNA molecules.
3. homologous chromosomes are paired-2048 molecules in total
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
• The banding patterns of these chromosomes are distinct from metaphase
chromosomes and have been associated with specific genes
• Metaphase chromosomes also have distinct bands, but these are thought to be
associated with genetically inactive heterochromatin DNA
• The term used to describe these chromosomes and similar chromosomes in
other diptera species is polytene chromosomes and these chromosomes
have primarily been used to:
1. to locate genes; and
2. to analyze structural changes in
chromosomes
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Duplications and Deletions
• A mechanisms that could generate a duplication is multiple replication of a
looped region of DNA by DNA polymerase
• That individual would have one chromosome with an extra copy of the
sequence whereas the homologous chromosome would still retain a single
copy of the sequence
• A second proposed molecular mechanism that can generate a duplication of a
chromosome by its very nature will also generate a deletion
• This mechanism is unequal crossing-over. This occurs when pairing occurs
between homologous chromosomes in regions that are out of register
• This pairing can be mediated by sequences that are repeated on the same
chromosome
• Following recombination (or crossing over) one chromosome will lose DNA
sequence whereas the homologous chromosome will gain the sequences lost
by the first
• The presence, and extent of a deletion, can be detected quite readily with
polytene chromosomes
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Duplications and Deletions
• A loop will appear on one paired chromosome, and those sequences found in
the looped region mark the length of the deletion
• Analysis of heterozygote chromosomes during pairing will also reveal a loop
structure, but without the band markers that are available with polytene
chromosomes, it is difficult to define the region
• It is easier to detect the larger deletions, but with good preparation and
patience, the deletion of a single band can be detected, and thus the
chromosomal location of a specific phenotype can be made
Evolution and Unequal Crossing Over
• One possible result of unequal crossing-over is the creation of a multigene
family. These are defined as a tandem array of genes that have similar function
• The best studied family is that which encodes the β-chain of human
hemoglobin. Six β-globin genes are found within 50 kb on chromosome 11
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Evolution and Unequal Crossing Over
• The one of β genes is a pseudogene that has a mutation which prevents its
expression. The sequences of these six genes are quite similar which suggests they
occurred by duplication of an ancestral β-globin gene
• Once a gene duplication event has occurred evolutionary constraints working upon
these gene presumably lessen
• First, another unequal crossing-over event could generate a third copy of the gene,
further expanding the family. Other similar events will further spread the family
• As the family expands, previous harmful mutations can now be tolerated because
functional copies will still exist
• Duplicate genes could now diversify and take on new or more specialized functions.
Thus, over evolutionary time the sequences of the family members can diverge, and
their role in phenotypic expression of the individual could change
• Deletions and duplications involve an actual gain or loss of genetic material by the
genome of the specific individual. If these changes are maintained and prove to
beneficial then eventually these changes might become stabilized in the species.
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Duplications of the Bar locus of Drosophila
•One phenotype that has been analyzed in Drosophila with respect to
duplications is bar eye. The eye of the fly is normally an elongated oval shape
whereas the bar eye phenotype is much thinner
•When the chromosomes of males with bar eye are analyzed, a duplication in
region 16A of the chromosome is detected
•Another mutant of the eye shape is the double bar eye. These individuals
have a second duplication of the same 16A region
Effects of duplications for region 16A of the X chromosome on the size of
the eyes in Drosophila.
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Inversions
• Another group of changes in chromosome structures are associated with a
relocation of the genetic material either within a chromosome or between nonhomologous chromosomes. These two types of changes are inversions and
translocations
• Inversions result when a segment of a chromosome is excised, inverted
180o, and reintegrated into the same chromosome. Two specific types of
inversions are recognized, and they are classified as to whether or not the
centromere is a portion of the inverted segment:
1. Paracentric inversion - an inversion of a segment of the chromosome
that does not involve the centromeric region
2. Pericentric inversion - an inversion of a segment of the chromosome
that involves the centromeric region
• In humans, it is difficult to detect inversions. If a large inversion occurs, then a
new banding pattern will be seen in the regions that under went the inversion
• One manner in which inversions can be detected is by a change in the
location of the centromere
Structure of an inversion. The chromosome has been broken at two points, and the
segment between them has been inverted.
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Inversions
• Inversions are not easily detected in homozygotes of other species, unless as with
humans, distinct chromosomal banding patterns have been established for normal
members of that species
• Heterozygotes derived from a cross of a normal individual and an individual with an
inversion in one chromosome will have specific patterns that occur because of pairing
problems
• In Drosophila, polytene chromosome will contain loops, evidence that one of the
synapsed chromosomes contains an inversion
• The appearance of meiotic chromosomes also will be affected if one of the
chromosomes has an inversion. Loops appear and define the region in which the
inversion has occurred
• Furthermore, if recombination occurs in a paracentric inversion region, then one-half of
the gametes will be normal and the other half will contain deleted chromosomes
• If the recombination involves a pericentric inversion then one-half of the gametes will
be normal with respect to the initial chromosomal arrangements and the other gametes
will contain chromosomes that contain both additions and deletions
Genetic Variation in Natural Pop. Cont...
VARIATION IN CHROMOSOME STRUCTURE
Inversions
• These abnormalities can generate unbalanced gametes and in general,
individuals with pericentric inversions are reproductively inferior
• In general, inversions do not change the phenotype of the individual unless an
excision site of the inversion is within the regulatory or structural region of a
gene
• The primary change that is seen with inversions is a change in linkage
relationships. A survey of 50 known paracentric inversions in humans revealed
that:
1. 14 chromosomes were involved
2. eight involved chromosome 3, 10 involved chromosome 7, and 7
involved chromosome 11
3. 34/50 appeared to familial
4. no harmful effects or reduced fertility of the
paracentric inversion noted
Translocation
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Translocation occur when a segment from one chromosome is
detached and reattached to a different (that is, nonhomologous )
chromosome.
Translocation
During meiosis these translocated
chromosomes would be expect to
pair with their untranslocated homologues in a cruciform, or crosslike
pattern.
This pairing configuration is
diagnostic of a translocation
heterozygote.