Download Lecture 11 - Lectures For UG-5

PRINCIPLES OF CROP PRODUCTION
(3 CREDIT HOURS)
LECTURE 11
CONTIG
SEQUENCE CONTIG
LINKAGE GROUP
LINKAGE ANALYSIS
GENETIC DRIFT
INTERFERENCE
LATERAL GENE TRANSFERS
CONTIG
• A contig (from contiguous) is a set of overlapping DNA
segments that together represent a consensus region of
DNA.
• In bottom-up sequencing projects, a contig refers to
overlapping sequence data (reads).
SEQUENCE CONTIGS
• A sequence contig is a contiguous, overlapping sequence
read resulting from the reassembly of the small DNA
fragments generated by bottom-up sequencing strategies.
• The bottom-up DNA sequencing strategy involves shearing
genomic DNA into many small fragments (bottom),
sequencing these fragments, reassembling them back into
contigs and eventually the entire genome (up).
• In bottom-up sequencing projects, amplified DNA is sheared
randomly into fragments appropriately sized for sequencing.
• The subsequent sequence reads, which are the data that
contains the sequence of each fragment, are assembled into
contigs, which are finally connected by sequencing the gaps
between them resulting in a sequenced genome.
SEQUENCE CONTIGS
• The ability to assemble contigs depends on the overlap of
reads.
• Because shearing is random and performed on multiple
copies of DNA, each portion of the genome should be
represented multiple times in different fragment frames.
• In other words, the sequences of the fragments (and thus
the reads) should overlap.
• After sequencing, the overlapping reads are assembled into
contigs by assembly software.
LINKAGE GROUP
• All the genes on a single chromosome.
• They are inherited as a group; that is, during cell division,
they act and move as a unit rather than independently.
• The existence of linkage groups is the reason some traits do
not comply with Mendel’s law of independent assortment,
i.e., the principle applies only if the genes are located on
different chromosomes.
• A linkage group is a collection of genes that are close enough
in a genome to be inherited together.
• The transcription and translation of genes in the group may
or may not be linked together.
• In simple cells lacking a nucleus called prokaryotes, the
genes that make up operons units can be considered linkage
groups.
LINKAGE GROUP
• Eukaryotes, more complex cells, do not have an equivalent structural
grouping in their genomes but despite a lack of operons, they can contain
many linkage groups
• Both prokaryotes and eukaryotes pass on linkage groups largely through
recombination.
• When a linkage group is involved in recombination, all the genes within the
group tend to stay together, so all of the genes’ activities are relocated at the
same time.
• This movement can be to a different place on the same chromosome or to a
different chromosome altogether.
• Usually, nucleic acid movement by recombination does not disrupt a linkage
group’s function.
• Linkage groups can be broken apart during recombination, but the
probability of that happening is fairly low.
LINKAGE ANALYSIS
• In this approach, the aim is to find out the rough location of the gene
relative to another DNA sequence called a genetic marker, which has its
position already known.
• All our chromosomes come in pairs, one inherited from our mother and
one from our father. Each pair of chromosomes contains the same genes
in the same order, but the sequences are not identical. This means it
should be easy to find out whether a particular sequence comes from
our mother or father. These sequence variants are called maternal and
parental alleles.
LINKAGE ANALYSIS
• In the case of the disease gene, the alternative alleles will be the normal
allele and the disease allele, and they can be distinguished by looking for
occurrences of the disease in a family tree or pedigree.
• Genetic markers are DNA sequences that show polymorphism (variation
in size or sequence) in the population.
• They are present in everyone and they can be typed (the allele can be
identified) using techniques such as the PCR.
• This ability to determine the parental origin of a DNA sequence allows us
to show whether recombination has taken place.
• Recombination occurs in germ cells-the cells that make eggs and sperms.
• In these cells, the maternal and paternal chromosomes pair up and
exchange parts.
• After recombination, the chromosomes contain a mixture of maternal
and paternal alleles.
LINKAGE ANALYSIS
• Diseased genes are mapped by measuring recombination against a panel
of different markers spread over the entire genome.
• In most cases, recombination will occur frequently, indicating that the
disease gene and marker are far apart.
• Some markers, however, due to their proximity, will tend not to
recombine with the disease gene and these are said to be linked to it.
• Ideally, close markers are identified that flank the disease gene and
define a candidate region of the genome between 1 and 5 million bp in
length.
• The gene responsible for the disease lies somewhere in this region.
A B
C
If A is the disease gene and B and C are genetic markers,
a b
c
recombination is likely to occur much more frequently
A
B
c
between A & C than it is
A B
C
a
b
C
between A & B. This allows
a
b
c
the disease gene to be mapped
relative to the markers B & C.
GENETIC DRIFT
• When the population is large, the impact of genetic drift is much milder.
When the reproductive population is small, however, the effects of
sampling error can alter the allele frequencies significantly.
• Genetic drift is therefore considered to be a consequential mechanism
of evolutionary change primarily within small, isolated populations.
• Although both processes affect evolution, genetic drift operates
randomly while natural selection functions non-randomly.
• While natural selection has a direction, guiding evolution towards
heritable adaptations to the current environment, genetic drift has no
direction and is guided only by the mathematics of chance.
• As a result, drift acts upon the genotypic frequencies within a
population without regard to their phenotypic effects.
• In contrast, selection favors the spread of alleles whose phenotypic
effects increase survival and/or reproduction of their carriers, lowers
the frequencies of alleles that cause unfavorable traits, and ignores
those that are neutral.
GENETIC DRIFT
• In natural populations, genetic drift and natural selection do not
act in isolation; both forces are always at play, together with
mutation and migration.
• However, the magnitude of drift on allele frequencies is larger
when the absolute number of copies of the allele is small, e.g., in
small populations.
• Genetic drift or allelic drift is the change in the frequency of a
gene variant (allele) in a population due to random sampling.
• The alleles in the offspring are a sample of those in the parents,
and chance has a role in determining whether a given individual
survives and reproduces.
• A population’s allele frequency is the fraction of the copies of one
gene that share a particular form.
• Genetic drift may cause gene variants to disappear completely
and thereby reduce genetic variation.
INTERFERENCE
• The effect of one crossing over event in altering the
probability of another crossing over event occurring at a
nearby location.
• This probability can be either increased (positive
interference) or decreased (negative interference) but the
latter is more usual.
• Positive Interference: one crossover event inhibits the
chances of another crossover event.
• Negative Interference: It increases the chance of a second
crossover.
INTERFERENCE
• Recombination is initiated by programmed double-strand
breaks (DSBs) of chromosomes.
• During the repair of some DSBs, chromosome arms are
exchanged generating crossovers (COs).
• In most organisms, COs are not distributed randomly.
• Closely spaced COs are observed less frequently than would
be expected from a random distribution. This phenomenon
is also known as crossover interference.
• Each chromosome typically receives at least one crossover,
which is known as “CO assurance”.
LATERAL GENE TRANSFERS
• Also called horizontal gene transfers.
• The transmission of genes between individual cells.
• These mechanisms not only generate new gene assortments,
they also help move genes throughout populations and from
species to species.
• The methods include transformation, transduction and
conjugation.
EPIGENETICS
• Relating to or arising from nongenetic influences on gene
expression.
• As an organism grows and develops, carefully orchestrated
chemical reactions activate and deactivate parts of the
genome at strategic times and in specific locations.
• Epigenetics is the study of these chemical reactions and the
factors that influence them.
THE END