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GENETIC MARKERS
Dr. S. S. SolankeyAssistant Professor-cum-Jr. Scientist
Department of Horticulture (Vegetable & Floriculture),Bihar Agricultural University, Sabour (Bhagalpur) – 813 210,
Bihar E-mail: [email protected]
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
Genetic Marker Morphological marker Molecular marker
1. Protein marker
2. DNA marker
Morphological
Molecular (DNA)
Protein (Isozymes)
Chromatografic, etc.
PCR Independent
PCR dependent
RFLP
AFLP,RAPD,Micro satellite,SNP, etc.
BiochemicalMarkers
Morphological MarkerMorphological Marker•Phenotypic markers•Naked eye marker
Fruit Size
Fruit Shape
Fruit Colour
• 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 polymorphismsb) DNA polymorphisms
Molecular markersR
e so l
utio
nR
e so l
utio
n po
we r
pow
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allozymes (protein-allozymes (protein-electrophoresis)electrophoresis)
RAPDRAPD(Random Amplified Polymorphic (Random Amplified Polymorphic DNA)DNA)
AFLPAFLP(Amplified Fragment Length (Amplified Fragment Length Polymorphism)Polymorphism)
Multi-locus fingerprints Multi-locus fingerprints (RFLP)(RFLP)
Microsatellites (SSRs)Microsatellites (SSRs)
SequencingSequencing (SNPs)(SNPs)
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)
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 configurationP 1 O 1 O 2
Dominant marker
Genetic marker characteristicsCharacteriCharacteri
sticssticsMorpholoMorpholo
gical gical markersmarkers
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
UnlimitedUnlimited HighHigh HighHigh
InheritancInheritancee
DominantDominant CodominaCodominantnt
CodominaCodominantnt
DominantDominant CodominaCodominantnt
CodominaCodominantnt
Positive Positive featuresfeatures
VisibleVisible Easy to Easy to detectdetect
Utilized Utilized before the before the latest latest technologitechnologies were es were availableavailable
Quick Quick assays assays with many with many markersmarkers
Well Well distributedistributed within d within the the genome, genome, many many polymorphpolymorphismism
Highly Highly distributedistributed within d within the the genome, genome, high high polymorphpolymorphismism
Negative Negative featuresfeatures
Possibly Possibly negative negative linkage to linkage to other other characterscharacters
Possibly Possibly tissue tissue specificspecific
RadioactivRadioactivity ity requiremerequirements, rather nts, rather expensiveexpensive
High basic High basic investmeninvestmentt
Long Long developmedevelopment of the nt of the markers, markers, expensiveexpensive
Long Long developmedevelopment of the nt of the markers, markers, expensiveexpensive
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