this ppt give insight on application of markers

1. Chapter five
Application of Markers
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2. Germplasm Characterization
It should first be assessed what the genetic
variability is within the organism being studied.
Analyze how identifiable particular genomic
sequence, near or in candidate genes.
Maps can be created to determine distances
between genes and differentiation between
species.
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3. Genetic markers can aid in the development of new
novel traits that can be put into mass production.
These novel traits can be identified using molecular
markers and maps.
Particular traits such as color, may be controlled by
just a few genes. Qualitative traits (requires less that
2 genes) such as color, can be identified using MAS
(marker assisted selection).
Once a desired marker is found, it is able to be
followed within different filial generations. An
identifiable marker may help follow particular traits
of interest when crossing between different genus
or species, with the hopes of transferring particular
traits to offspring.
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4. One example of using molecular markers in
identifying a particular trait within a plant is,
Fusarium head blight in wheat.
Fusarium head blight can be a devastating disease in
cereal crops but certain varieties or offspring or
varieties may be resistant to the disease.
This resistance is inferred by a particular gene that
can be followed using MAS (Marker Assisted
Selection) and QTL (Quantitative Trait Loci).
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5. • QTL's identify particular variants within
phenotypes or traits and typically identify where the
GOI (Gene of interest) is located.
• Once the cross has been made, sampling of
offspring may be taken and evaluated to determine
which offspring inherited the traits and which
offspring did not.
• This type of selection is becoming more beneficial
to breeders and farmers because it is reducing the
amount of pesticides, fungicides and insecticides.
• Another way to insert a GOI is through mechanical
or bacterial transmission. This is more difficult but
may save time and money.
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6. Applications of markers in breeding
1. Assessing variability of genetic differences
and characteristics within a species
2. Identification and fingerprinting of
genotypes
3. Estimating distances between species and
offspring
4. Identifying location of QTL's
5. Identification of DNA sequence from useful
candidate genes.
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7. • Gene mapping
• Pre and post natal
diagnosis of
diseases
• Anthropological
and molecular
evolution studies
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8. Genetic Diversity Conservation:
Consequent upon the rampant(uncontrolled
spreading) crossbreeding of exotic animals with
local breeds in order to exploit heterosis, there has
been an irreversible loss of genetic diversity among
our local animal breeds.
The conservation of genetic diversity is important
in the sense that it encourages high level of
heterozygosity in the population.
Genetic variation is a prerequisite for populations
to be able to face future environmental changes.
Genetic diversity is necessary to ensure long-term
response to selection, either natural or artificial, for
traits of economic or cultural interest.
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9. • Potentially unique genes in populations should
be conserved with studies using DNA markers,
as their contribution to biodiversity would be
greater.
• The primary aim of studying genetic diversity is
to understand the extent of differentiation of
populations within species.
• Population-specific genetic markers (alleles) can
be generated using a range of methods available
for detection of polymorphic loci.
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10. • The genetic characterization of populations,
breeds and species allows evaluation of genetic
variability. Molecular markers have been
exploited to access this variability as they
contribute information on every region of the
genome.
• The most widely used molecular techniques for
the study of genetic variations at the DNA level
include RFLP, RAPD, AFLP, microsatellites and
mini-satellites.
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11. Expression profile Analysis
• Gene expression monitoring currently is the most
widespread application of Molecular Markers such as
microarrays.
• Microarray assays may be directly integrated into
functional genomic approaches aimed both at assigning
function to identified genes, and to studying the
organization and control of genetic pathways acting
together to make up the functional organism.
• The rationale behind this approach is that genes showing
similarity in expression pattern may be functionally
related and under the same genetic control mechanism.
• At present, both cDNA microarrays and oligonucleotide
microarrays are used for gene expression monitoring.
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12. • Gene expression
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13. Identification of Disease Carrier:
• Infectious diseases are responsible for great
losses in economic returns to the livestock
farmer.
• Most of the serious incurable diseases result not
from infectious disease-causing organisms but
by defective genomes of the individual animals.
• Certain allelic variations in the host genome lead
to susceptibility or resistance to a particular
disease.
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14. • DNA polymorphism occurring within a gene helps
to understand the molecular mechanism and genetic
control of several genetic and metabolic disorders
and allows the identification of heterozygous
carrier –animals which are otherwise phenotypically
indistinguishable from normal individuals.
• The PCR-RFLP assay has been used to identify
carrier animals possessing the defective recessive
allele in:
- bovine leucocyte adhesion deficiency in cattle,
- hyperkalemic periodic analysis in horses and
- malignant hyperthermia in pigs. Carrier animals of
weaver disease in cattle using microsatellite (TGLA
116) marker.
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15. Determination of Parentage:
• The identification of parentage in segregating
populations generally takes place by means of the
exclusion principle. That is, presence at some
genetic locus in the offspring of an allele not found
in either of the putative parents effectively excludes
the particular parental pair from biological
parenthood.
• Highly polymorphic DNA fingerprinting markers
have been reported to be very useful in parentage
testing.
• Molecular markers can be employed for sire
identification in Artificial Insemination
programmes.
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16. Marker-Assisted Selection:
 This is a genetic engineering technique which involves the
incorporation of DNA markers for selection, to increase
the efficiency of the traditional methods of breeding
based on phenotypic information.
 Molecular marker analysis allows the identification of:
- genome segments,
- QTL contributing to the genetic variance of a trait
and
- thus to select superior genotype by environment
interaction.
 Therefore selection for favorable QTL effects based on
molecular marker studies has great benefits to offer for
the improvement of such economic traits.
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17. Transgenesis:
• This is a procedure in which a gene or part of a
gene from one individual is incorporated into the
genome of another one.
• The starting point of this technology is the
identification of the genes of interest. In this
context, molecular markers can serve as points of
reference for mapping the relevant genes that would
be the first step towards their manipulation.
• Molecular markers could as well be used to identify
animals carrying the transgenes for the purpose of
multiplication.
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18. Sex Determination of Offspring:
• Molecular markers can be applied in the determination of
sex of pre-implantation embryos.
• This can be achieved by using as probes, Y-chromosome-
specific (male-specific) DNA sequence.
• Using the PCR-based method of sex determination has
the advantage of being carried out in less than five hours
with almost 100% accuracy.
• It is less invasive, unlike other cytogenetical methods, and
can be done at an early stage of the embryo. The sexing
of pre-implantation embryos can serve as an important
tool for improving a herd for a desired purpose.
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