Genetic markers-SSS

A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species that can be described as a variation (i.e. mutation or alteration in the genomic loci) that can be observed. It may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites (SSR).

1. GENETIC MARKERS
Dr. S. S. Solankey
Assistant Professor-cum-Jr. Scientist
Department of Horticulture (Vegetable & Floriculture),
Bihar Agricultural University, Sabour (Bhagalpur) – 813 210, Bihar
E-mail: [email protected]

2. Marker
Gene of known function and location
Gene that allows studying the inheritance of that gene
Genetic information resides in the genome
Genetic Marker
Any phenotypic difference controlled by genes, that can be used
for studying recombination processes or selection of a more or
less closely associated target gene
Anything in the genome that is variable and can be used to
compare individuals
Detectable allelic variation on a chromosome can be a phenotype,
can also be a unique detectable sequence of DNA

3. Genetic Marker
Morphological marker
Molecular marker
1. Protein marker
2. DNA marker

4. Morphological
Molecular
(DNA)
Protein (Isozymes)
Chromatografic, etc.
PCR Independent
PCR
dependent
RFLP
AFLP,
RAPD,
Micro satellite,
SNP, etc.
BiochemicalMarkers

5. Morphological MarkerMorphological Marker
•Phenotypic markers
•Naked eye marker
Fruit Size
Fruit Shape
Fruit Colour

6. •Readily detectable sequence of protein or DNA that are closely
linked to a gene locus and/or a morphological or other
characters of a plant
•Readily detectable sequence of protein or DNA whose
inheritance can be monitored and associated with the trait
inheritance independently from the environment
Molecular Markers
Types:
a) protein polymorphisms
b) DNA polymorphisms

7. Molecular markers
R
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allozymes (protein-electrophoresis)allozymes (protein-electrophoresis)
RAPDRAPD
(Random Amplified Polymorphic DNA)(Random Amplified Polymorphic DNA)
AFLPAFLP
(Amplified Fragment Length Polymorphism)(Amplified Fragment Length Polymorphism)
Multi-locus fingerprints (RFLP)Multi-locus fingerprints (RFLP)
Microsatellites (SSRs)Microsatellites (SSRs)
SequencingSequencing (SNPs)(SNPs)

8. PCR Based markersPCR Based markers
Single Nucleotide Polymorphisms (SNPs)
Simple Sequence Repeat (SSR)
AFLP (Amplified Fragment Length Polymorphism)
RAPD (Random Amplified Polymorphic DNA)
Non-PCR Based markerNon-PCR Based marker
RFLP (Restriction Fragment Length Polymorphism)

9. Polymorphism
-Parent 1 : one band
-Parent 2 : a smaller band
-Offspring 1 : heterozygote = both bands
-Offspring 2 : homozygote parent 1

Polymorphism
Parent 1 : one band
-Parent 2 : no band
-Offspring 1 : homozygote parent 1
-Offspring 2 : ????
P
2
P
1
O
2
O
1
Gel configuration
Co-dominant marker
P
2
Gel configuration
P
1 O
1
O
2
Dominant marker

10. Genetic marker characteristics
CharacteristicCharacteristic
ss
MorphologicaMorphologica
l markersl markers
Protein Protein
markersmarkers
RFLP RFLP
markersmarkers
RAPD RAPD
markersmarkers
SSR SSR
markersmarkers
SNP SNP
MarkersMarkers
Number of Number of
lociloci
LimitedLimited LimitedLimited Almost Almost
unlimitedunlimited
UnlimitedUnlimitedHighHigh HighHigh
InheritanceInheritanceDominantDominant CodominantCodominantCodominantCodominantDominantDominant CodominantCodominantCodominantCodominant
Positive Positive
featuresfeatures
VisibleVisible Easy to detectEasy to detectUtilized Utilized
before the before the
latest latest
technologies technologies
were availablewere available
Quick assays Quick assays
with many with many
markersmarkers
Well Well
distributed distributed
within the within the
genome, genome,
many many
polymorphispolymorphis
mm
Highly Highly
distributed distributed
within the within the
genome, high genome, high
polymorphispolymorphis
mm
Negative Negative
featuresfeatures
Possibly Possibly
negative negative
linkage to linkage to
other other
characterscharacters
Possibly Possibly
tissue specifictissue specific
Radioactivity Radioactivity
requirements, requirements,
rather rather
expensiveexpensive
High basic High basic
investmentinvestment
Long Long
development development
of the of the
markers, markers,
expensiveexpensive
Long Long
development development
of the of the
markers, markers,
expensiveexpensive

11.  Polymorphic
 Co-dominant inheritance
 Occurs throughout the genome
 Reproducible
 Easy, fast and cheap to detect
 Selectivity neutral
 High resolution with large number of samples
Desirable properties of
molecular marker