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: shashank.hort@gmail.com

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
ResolutionResolutionpowerpower
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 2P 1 O 2O 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
ProteinProtein
markersmarkers
RFLPRFLP
markersmarkers
RAPDRAPD
markersmarkers
SSRSSR
markersmarkers
SNPSNP
MarkersMarkers
Number ofNumber of
lociloci
LimitedLimited LimitedLimited AlmostAlmost
unlimitedunlimited
UnlimitedUnlimited HighHigh HighHigh
InheritanceInheritance DominantDominant CodominantCodominant CodominantCodominant DominantDominant CodominantCodominant CodominantCodominant
PositivePositive
featuresfeatures
VisibleVisible Easy to detectEasy to detect UtilizedUtilized
before thebefore the
latestlatest
technologiestechnologies
were availablewere available
Quick assaysQuick assays
with manywith many
markersmarkers
WellWell
distributeddistributed
within thewithin the
genome,genome,
manymany
polymorphispolymorphis
mm
HighlyHighly
distributeddistributed
within thewithin the
genome, highgenome, high
polymorphispolymorphis
mm
NegativeNegative
featuresfeatures
PossiblyPossibly
negativenegative
linkage tolinkage to
otherother
characterscharacters
PossiblyPossibly
tissue specifictissue specific
RadioactivityRadioactivity
requirements,requirements,
ratherrather
expensiveexpensive
High basicHigh basic
investmentinvestment
LongLong
developmentdevelopment
of theof the
markers,markers,
expensiveexpensive
LongLong
developmentdevelopment
of theof 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