Skip to main content

SSR (Simple Sequence Repeat) Marker


SSR (Simple Sequence Repeat) Markers –

Detailed Notes


Introduction


SSR markers, also called microsatellites, are short tandem repeats (1–6 bp) of DNA sequences found throughout the genome.
Examples: (A)n, (CA)n, (GATA)n, where n is the number of repeat units.
SSRs are highly polymorphic, co-dominant, and locus-specific, widely used in genetic mapping, variety identification, population genetics, and marker-assisted selection (MAS).
SSRs are similar to STRs; in plants and animals, the term SSR is more commonly used in molecular breeding, while STR is used more in forensics and human genetics.


Structure of SSR


Repeat motif: 1–6 bp
Number of repeats: Variable among individuals → basis of polymorphism
Flanking regions: Conserved sequences used to design specific PCR primers
SSR loci are generally abundant in non-coding regions, though some occur in genes.
Principle
SSR markers exploit variation in the number of repeat units at a specific locus.
PCR amplification using primers flanking the SSR locus produces fragments of different lengths, reflecting the number of repeats.
These length differences are detected through gel electrophoresis or capillary electrophoresis, allowing genotyping and polymorphism analysis.


Key idea:


Conserved flanking sequences → PCR amplification → Fragment size variation → Allele determination → Genetic analysis
Materials Required
Genomic DNA
SSR-specific primers (flanking repeats)
PCR reagents: Taq polymerase, dNTPs, buffer, Mg²⁺
Thermal cycler
Electrophoresis system: Polyacrylamide gel or capillary electrophoresis
DNA stains: Ethidium bromide, SYBR Green, or fluorescent labeling.


Procedure


Step 1: DNA Isolation

Extract high-quality DNA from blood, leaf, seed, tissue, or other biological samples.

Step 2: Primer Design

Identify SSR loci in genomic sequences.
Design primers flanking the repeat motif for locus-specific amplification.


Step 3: PCR Amplification


Set up PCR with DNA, primers, Taq polymerase, buffer, and dNTPs.
PCR cycles:
Denaturation: 94–95°C
Annealing: 50–60°C (primer-dependent)
Extension: 72°C
25–35 cycles typical for good amplification.

Step 4: Fragment Analysis


Separate PCR products based on size differences:
Polyacrylamide gel electrophoresis (high resolution)
Capillary electrophoresis (fluorescent detection)
Determine allele size corresponding to the number of repeat


Step 5: Data Analysis


Genotype individuals based on allelic patterns
Calculate heterozygosity, polymorphism information content (PIC), or genetic diversity
Apply results in breeding, mapping, or diversity studies
Characteristics of SSR Markers


Highly polymorphic → variation in repeat number
Co-dominant marker → distinguish homozygotes and heterozygotes
PCR-based, requires small DNA amounts
Locus-specific and reproducible
Abundant in non-coding regions, occasionally in genes

Merits


High polymorphism, suitable for genotyping and diversity studies
Co-dominant, can detect heterozygosity
PCR-based, works with small or degraded DNA
Locus-specific and reproducible
Useful for genetic mapping, MAS, population genetics, and variety identification.

Limitations

Requires sequence information for primer design
PCR inhibitors in samples may affect amplification
High mutation rate in repeats may complicate evolutionary studies
Equipment for high-resolution electrophoresis can be expensive
Development of SSR markers can be labor-intensive and costly

Applications

Genetic mapping and linkage analysis in plants and animals
Marker-assisted selection (MAS) for traits like disease resistance, yield, or stress tolerance
Variety and cultivar identification in crop breeding
Population genetics: genetic diversity, gene flow, inbreeding analysis
Conservation biology: individual identification in endangered species
Can be used in human and animal genetics for trait or disease association studies

Conclusion


SSR markers are powerful, co-dominant, and highly polymorphic markers widely used in plant and animal breeding, genetic mapping, and population genetics.
They provide high-resolution, reproducible, locus-specific genotyping, but require prior sequence knowledge and specialized equipment for analysis.



SSR (Simple Sequence Repeat) MCQs


What does SSR stand for in molecular biology?
a) Single Sequence Repeat
b) Simple Sequence Repeat ✅
c) Short Strand RNA
d) Single Strand Replication
SSR markers are also known as:
a) RFLP
b) Microsatellites ✅
c) AFLP
d) RAPD
What type of sequences do SSRs consist of?
a) Repeated DNA motifs of 1–6 bp ✅
b) Long stretches of 100–200 bp
c) Protein-coding regions
d) RNA sequences
SSR markers are highly polymorphic due to:
a) Point mutations
b) Variation in repeat number ✅
c) Large insertions
d) Gene duplications
Which genome regions commonly contain SSRs?
a) Exons
b) Introns and non-coding regions ✅
c) Ribosomal RNA genes
d) Only mitochondrial DNA
Which technique is commonly used to detect SSRs?
a) PCR ✅
b) Southern blot
c) ELISA
d) Western blot
What is the main advantage of SSR markers over RAPD?
a) Dominant markers
b) Co-dominant and highly reproducible ✅
c) Random amplification
d) Require radioactive labeling
SSR primers are designed to:
a) Amplify the repeat region ✅
b) Bind to RNA
c) Cut DNA
d) Sequence proteins
SSR markers are co-dominant. This means:
a) Can distinguish homozygous and heterozygous genotypes ✅
b) Only dominant alleles can be detected
c) Detects only coding regions
d) Cannot be used for mapping
SSR markers are especially useful for:
a) Protein analysis
b) Gene mapping and diversity studies ✅
c) RNA splicing analysis
d) Chromosome staining
A dinucleotide repeat in SSR means:
a) 2 bp motif repeated ✅
b) 3 bp motif repeated
c) 4 bp motif repeated
d) 6 bp motif repeated
Which of these is a trinucleotide SSR motif?
a) (CA)n
b) (CAG)n ✅
c) (AT)n
d) (G)n
SSR markers require which kind of DNA template?
a) RNA
b) High-quality genomic DNA ✅
c) Protein extracts
d) Plasmid only
Which of the following is NOT an advantage of SSR markers?
a) High polymorphism
b) Co-dominant inheritance
c) Low reproducibility ✅
d) Genome-wide distribution
SSR markers are inherited in a:
a) Maternal fashion
b) Mendelian fashion ✅
c) Random fashion
d) Cytoplasmic fashion
SSR length variations are caused by:
a) Point mutation
b) Slipped-strand mispairing ✅
c) Large chromosomal rearrangements
d) RNA editing
Which type of repeats is most abundant in eukaryotic genomes?
a) Mononucleotide
b) Dinucleotide ✅
c) Trinucleotide
d) Tetranucleotide
SSR markers can be used for:
a) Marker-assisted selection ✅
b) RNA transcription
c) Protein folding
d) Metabolic profiling
SSR detection by PCR requires primers flanking:
a) Only coding sequences
b) The repeat region ✅
c) Random DNA sequences
d) Mitochondrial DNA
SSR analysis is often visualized by:
a) Gel electrophoresis ✅
b) ELISA
c) Mass spectrometry
d) Flow cytometry
The number of SSR alleles per locus is usually:
a) Low
b) High ✅
c) Always 2
d) None
SSR markers are particularly useful in:
a) Cloning genes
b) Population genetics studies ✅
c) Protein sequencing
d) RNA interference
Which factor affects SSR polymorphism?
a) Repeat motif length ✅
b) Primer length
c) DNA extraction method
d) RNA concentration
A tetranucleotide SSR has:
a) 2 bp repeats
b) 4 bp repeats ✅
c) 3 bp repeats
d) 1 bp repeat
SSR markers can detect heterozygosity because:
a) They are dominant
b) They are co-dominant ✅
c) They mutate slowly
d) They are in coding regions
Which type of SSR is most stable?
a) Mononucleotide
b) Dinucleotide
c) Trinucleotide ✅
d) Hexanucleotide
SSR markers are expensive because:
a) Require radioactive labeling
b) Need sequence information for primer design ✅
c) Cannot be amplified
d) Only work in bacteria
SSR marker length is measured in:
a) Base pairs (bp) ✅
b) Amino acids
c) Kilodaltons
d) Nucleotides per microliter
SSR markers are ideal for:
a) Detecting large chromosomal changes
b) Fine mapping of traits ✅
c) Protein analysis
d) RNA splicing
Which of the following is a limitation of SSR markers?
a) Low polymorphism
b) Requires prior sequence information ✅
c) Cannot detect heterozygotes
d) Only used in bacteria
SSR markers can be used to study:
a) Gene expression
b) Genetic diversity ✅
c) Protein folding
d) RNA transcription
Which of these plants is widely studied using SSRs?
a) Arabidopsis ✅
b) E. coli
c) S. cerevisiae
d) Drosophila
SSR markers are sometimes labeled with:
a) Fluorescent dyes ✅
b) Enzymes only
c) Radioactive proteins
d) Antibodies
The main source of SSR polymorphism is:
a) Environmental factors
b) Variation in repeat number ✅
c) Epigenetic changes
d) RNA interference
SSR markers can be used in animals for:
a) Paternity testing ✅
b) Protein analysis
c) Metabolic profiling
d) RNA transcription
The first step in SSR analysis is:
a) RNA extraction
b) DNA isolation ✅
c) Protein purification
d) Southern blotting
SSR markers are more informative than RAPD because:
a) They are dominant
b) They are co-dominant and reproducible ✅
c) They require no primers
d) They detect fewer loci
Microsatellites are distributed in:
a) Exons
b) Introns and intergenic regions ✅
c) Only promoters
d) Only ribosomal DNA
SSR markers help in constructing:
a) Protein structure
b) Genetic linkage maps ✅
c) RNA secondary structure
d) Chromosome staining
SSR primers are usually:
a) 10–25 nucleotides long ✅
b) 50–100 nucleotides
c) 1–5 nucleotides
d) 100–200 nucleotides
Which type of repeat is least polymorphic?
a) Mononucleotide ✅
b) Dinucleotide
c) Trinucleotide
d) Tetranucleotide
SSR markers are also useful in:
a) Forensic identification ✅
b) RNA sequencing
c) Enzyme kinetics
d) Protein crystallography
Which of the following is an example of a dinucleotide repeat?
a) (CA)n ✅
b) (CAG)n
c) (GATA)n
d) (ATG)n
SSR polymorphism can be analyzed using:
a) Polyacrylamide gel electrophoresis ✅
b) Western blot
c) ELISA
d) Flow cytometry
SSR markers are considered:
a) Low-throughput
b) Highly reliable and reproducible ✅
c) Non-informative
d) Dominant
Which factor increases SSR mutation rate?
a) Longer repeats ✅
b) Short repeats
c) GC content only
d) Protein coding region
SSR-based maps are useful for:
a) Metabolic engineering
b) Quantitative trait locus (QTL) mapping ✅
c) RNA splicing
d) Protein folding
SSR detection can be automated using:
a) Fluorescent capillary electrophoresis ✅
b) ELISA
c) Northern blot
d) Spectrophotometry
SSR markers are less affected by:
a) Environmental conditions ✅
b) DNA quality
c) PCR conditions
d) Repeat length
SSR markers can be used in:
a) Plants, animals, and microbes ✅
b) Only plants
c) Only animals
d) Only bacteria




Comments

Post a Comment

Popular Posts

DNA FOOTPRINTING

DNA FOOTPRINTING Introduction DNA footprinting is a molecular biology technique used to identify the specific site(s) on DNA where proteins (such as transcription factors) bind. It reveals the exact nucleotide sequences protected by bound proteins against cleavage by nucleases or chemical agents. It is widely used to study DNA-protein interactions, transcription regulation, and gene expression control. Definition DNA footprinting: A technique used to locate the binding site of DNA-binding proteins on DNA by detecting protected regions that are resistant to enzymatic or chemical cleavage. Principle DNA-binding proteins protect the DNA segment they occupy. DNA exposed to nucleases (DNase I) or chemical cleavage agents is cut at accessible regions. Regions bound by protein remain unaffected, leaving a “footprint”. When fragments are separated on a denaturing polyacrylamide gel, the missing bands correspond to protein-binding sites. Key idea: Cleavage occurs everywhere except where the pro...
Post a Comment
Read more

❥ Southern Blotting Notes

Southern Blotting  ❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥  Introduction Southern blotting is a molecular biology technique used for the detection of specific DNA sequences in a complex mixture of DNA. It was developed by Edwin M. Southern in 1975. The method involves restriction digestion of DNA, separation by gel electrophoresis, transfer (blotting) onto a membrane, and hybridization with a labeled DNA probe. Principle of Southern Blotting The technique is based on the principle of complementary base pairing. A single-stranded labeled DNA probe hybridizes specifically with its complementary DNA sequence immobilized on a membrane. Detection of the label confirms the presence and size of the target DNA fragment. Steps Involved in Southern Blotting. 1. Isolation of DNA Genomic DNA is extracted from cells or tissues. DNA must be pure and intact to ensure accurate results. 2. Restriction Enzyme  Digestion DNA is digested using specific restriction endonucleases. Produces DNA f...
1 comment
Read more

RESTRICTION MAPPING

RESTRICTION MAPPING Introduction Restriction mapping is a molecular biology technique used to determine the relative positions of restriction enzyme recognition sites on a DNA molecule. It involves digestion of DNA with one or more restriction endonucleases followed by analysis of fragment sizes using agarose gel electrophoresis. Restriction mapping is essential for DNA characterization, cloning strategies, gene localization, and genome analysis. Definition Restriction mapping is the process of identifying the number, order, and distances between restriction enzyme cleavage sites within a DNA fragment by analyzing the pattern of fragments generated after enzymatic digestion. Principle Restriction enzymes cut DNA at specific palindromic nucleotide sequences. When DNA is digested with: Single restriction enzyme → produces fragments based on its recognition sites Multiple restriction enzymes → produces fragments whose sizes reveal the relative positions of sites By comparing fragment size...
Post a Comment
Read more

π“†ž Western Blotting Notes

Western Blotting (Immunoblotting) ❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥ π“†ž❥  Introduction Western blotting, also known as immunoblotting, is a widely used analytical technique for the detection, identification, and quantification of specific proteins in a complex biological sample. The technique combines protein separation by gel electrophoresis with specific antigen–antibody interaction. The method was developed by Towbin et al. (1979) (Burnette 1981---its group work) and is called “Western” in analogy to Southern blotting (DNA) and Northern blotting (RNA). Principle The principle of Western blotting involves: Separation of proteins based on molecular weight using SDS-PAGE Transfer (blotting) of separated proteins onto a membrane Specific detection of the target protein using primary and secondary antibodies Visualization using enzymatic or fluorescent detection systems πŸ‘‰ Antigen–antibody specificity is the core principle of Western blotting. Steps Involved in Western Blotting 1. Sa...
Post a Comment
Read more

Protein Structure Database (PDB)

Protein Structure Database (PDB) Introduction The Protein Structure Database (PDB) is the primary global repository for the three-dimensional (3D) structures of biological macromolecules such as proteins, nucleic acids, and protein–ligand complexes. These structures are determined experimentally using techniques like X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and Cryo-Electron Microscopy (Cryo-EM). PDB plays a vital role in understanding: Protein structure and function Molecular interactions Drug discovery and design Structural biology and bioinformatics History and Development Established in 1971 Founded by Brookhaven National Laboratory (USA) Initially contained only 7 protein structures Now maintained by the Worldwide Protein Data Bank (wwPDB) Members of wwPDB RCSB PDB (USA) PDBe (Europe) PDBj (Japan) BMRB (Biological Magnetic Resonance Data Bank) Objectives of PDB To collect, store, and distribute 3D structural data of biomolecules To provide free and ope...
Post a Comment
Read more

••CLASSIFICATION OF ALGAE - FRITSCH

      MODULE -1       PHYCOLOGY  CLASSIFICATION OF ALGAE - FRITSCH  ❖F.E. Fritsch (1935, 1945) in his book“The Structure and  Reproduction of the Algae”proposed a system of classification of  algae. He treated algae giving rank of division and divided it into 11  classes. His classification of algae is mainly based upon characters of  pigments, flagella and reserve food material.     Classification of Fritsch was based on the following criteria o Pigmentation. o Types of flagella  o Assimilatory products  o Thallus structure  o Method of reproduction          Fritsch divided algae into the following 11 classes  1. Chlorophyceae  2. Xanthophyceae  3. Chrysophyceae  4. Bacillariophyceae  5. Cryptophyceae  6. Dinophyceae  7. Chloromonadineae  8. Euglenineae    9. Phaeophyceae  10. Rhodophyceae  11. Myxophyce...
Post a Comment
Read more

✩‧₊ Plaque Blotting Technique

Plaque Blotting Technique *ੈ✩‧₊˚༺☆༻*ੈ✩‧₊˚*ੈ✩‧₊˚༺☆༻*ੈ✩‧₊˚ Introduction Plaque blotting is a molecular biology screening technique used to identify specific DNA or RNA sequences present in bacteriophage plaques formed on a bacterial lawn. It is especially useful in the screening of recombinant phage libraries such as Ξ» (lambda) phage genomic or cDNA libraries. This technique combines: Plaque assay (to isolate individual phage clones) Blotting technique (to transfer nucleic acids onto a membrane) Hybridization (to detect specific sequences using labeled probes) Principle of Plaque Blotting The principle of plaque blotting is based on nucleic acid hybridization. Each plaque represents a clone of phage particles containing identical DNA. DNA from phage particles in plaques is: Released Denatured into single strands Transferred onto a nitrocellulose or nylon membrane The membrane is incubated with a labeled DNA/RNA probe complementary to the target sequence. Hybridization between probe and t...
Post a Comment
Read more

Biological Databases – Types of Data and DatabasesNucleotide Sequence Databases (EMBL, GenBank, DDBJ)

Biological Databases – Types of Data and Databases Nucleotide Sequence Databases (EMBL, GenBank, DDBJ) 1. Introduction Biological databases are systematic, computerized collections of biological information that allow efficient storage, retrieval, updating, and analysis of large volumes of biological data. With the advent of genome sequencing, molecular biology, and bioinformatics, biological databases have become essential tools in biological research. These databases support studies in genomics, proteomics, evolutionary biology, taxonomy, medicine, agriculture, and biotechnology. 2. Types of Data Stored in Biological Databases Biological databases store diverse types of biological information, including: 1. Sequence Data DNA sequences RNA sequences Protein sequences 2. Structural Data Three-dimensional structures of proteins Nucleic acid structures 3. Functional Data Gene functions Enzyme activity Regulatory elements 4. Genomic Annotation Data Gene location Exons, introns Promoters a...
Post a Comment
Read more