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: shashank.hort@gmail.com

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

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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