intro to morphological, biochemical and molecular markers.pdf

introduction to genome mapping
genetic map
genetic markers
morphological markers
biochemical markers
molecular markers

1. GENOMICS

2. •The molecular characterization of whole genomes aims to understand
the molecular organization and information content of the entire
genome and of the products that the genome encodes
•Genome: The entire complement of genetic material in a
chromosome set.
•Genome mapping: To determine the relative positions of, and the
distance between genes or different parts of the genetic material in a
chromosome set.
•Molecular mapping aids in identifying the location of particular
markers within the genome.

3. Genomics
Structural
Genomics
Functional
Genomics
Characterizing the
physical nature of whole
genomes
Characterizing the
proteome and over all
patterns of gene
expression

4. •A catalog at the nucleotide (and
amino acid) sequence levels of all the
genes and gene products encoded by
the genome will provide the raw
material that can serve as sources of
insight into everything ,from practical
matters of human disease and
agricultural genetics to basic
biological phenomena such as thos
underlying cell physiology,
development , behavior , ecology and
evolution

5. Steps to make genetic map
Markers to
generate
highly
saturated map
Physical map
Sequencing
for the whole
genome

6. Steps to make genetic map
Markers to
generate
highly
saturated map
Physical map
Sequencing
for the whole
genome

7. Genetic
markers
Morphological
markers
Biochemical
markers
Molecular
markers

8. Genetic
markers
Morphological
markers
Biochemical
markers
Molecular
markers

9. Morphological markers
•physical or structural features
of an organism that can be
used to identify or classify it.
•The 1st genetic maps were
based on morphological or
phenotypic markers.

10. pace of progress was slow
The paucity of such
markers.
Maps were
developed from the
analysis of multiple
crosses.
Some markers were
of limited value due
to epistatic and
pleiotropic effects.
Mapping a new
gene was a
laborious time-
consuming process.

11. Genetic
markers
Morphological
markers
Biochemical
markers
Molecular
markers

12. Biochemical Markers
•Called biomarkers
•Have the advantage that many of the relevant genes have multiple
alleles.
Example :
In human : The gene HLA-DRB1 has at least 290 allele and HLA-B has
over 400 alleles

13. Biochemical Markers advantages
Co-dominant
markers.
Less price

14. Biochemical Markers Applications:
Linkage
mapping.
Population
studies

15. Biochemical Markers
Disadvantages
Sex limited
Age dependent
(change with the
developmental
stage)
Influenced by
environment
it covers less than
10% of the
genome
Require prior
information
Low
polymerrphism
power

16. Gene maps are not very comprehensive
Because Genes are very useful markers, but they are by no means
ideal:
•In most eukaryotic genomes the genes are widely spaced out with
large gaps between them.
•Only a fraction of the total number of genes, exist in allele forms that
can be distinguished conveniently.

17. Genetic
markers
Morphological
markers
Biochemical
markers
Molecular
markers

18. Genetic
markers
Morphological
markers
Biochemical
markers
Molecular
markers

19. Molecular Markers
•Reflect heritable differences in homologous DNA sequences among
individuals.
•These differences result from:
Base-pair
changes.
Rearrangements
(translocation
and inversion) .
Insertions or
deletions.
Variation in
number of
tandem repeats .

20. ADVANTAGES OF MOLECULAR
MARKERS
Ubiquitous.
Inherited in a
Mendelian
fashion.
High level of
polymorphism.
Free of
environmental
variation.
Detectable in
all tissues at
any stage.
Revealing
variation at a
DNA level

21. Characteristics
Nondestructive
assay.
Early onset of
phenotypic
expression
Random
distribution
throughout the
genome .
Assay can be
automated.
DNA has long
shelf-life .
readily
exchangeable b/w
labs

22. DNA markers
Hybridization
based markers
RFLPs MinisatellitesMicrosatellites
PCR-based
markers
RAPDs MP-PCR AFLPs SSRs SCoT

23. Genetic
markers
Morphological Biochemical Molecular
Single locus
markers
RFLP Microsatellite SNPs
Multi locus
markers
ISSR AFLP SCoT RAPD