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Example of ISSR genotyping of endangered plants using an optimized workflow. Click to enlarge.

Inter-simple sequence repeat (ISSR) analysis is a technique commonly used for identification of individuals, mostly plant species, based on variation found in the regions between microsatellites. ISSR-PCR uses a single fluorescently labeled primer to target and amplify the region between identical microsatellites. The result is a mix of short, amplified DNA strands that vary widely in length.

This method has a wide range of research applications, including the characterization of genetic relatedness among populations, genetic fingerprinting, gene tagging, detection of clonal variation, cultivar identification, phylogenetic analysis, detection of genomic instability, and assessment of hybridization.

Step-by-Step Guide to Microsatellite ISSR Analysis

DNA Purification kit

DNA extraction is a critical first step in the experimental workflow of DNA Sequencing and Fragment analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.

Recommended Products: DNA Isolation


Amplify the target by PCR using fluorescent labeled primer.

Recommended Products: Design Primer & Perform PCR

Fragment Analysis sizing graph image.

Add aliquot of PCR product to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.

Recommended Products: Prepare Sample for Analysis

Sizing Information

To learn more about our GeneScan Size standards used in sizing experiments please see our table below.

When DNA fragments are labeled with: Choose a size standards labeled with: Recommended Size Standard Possible Applications Other Kits and Products
dR110, dR6G, dTAMRA™, dROX (Dye Set DS-02 - Filter E5) LIZ®
GeneScan™ 120 LIZ® Size Standard
GeneScan™ 600 LIZ Size Standard v2.0
Microsatellite, LOH, ISSR, Chimerism, ISSR, RFLP, T-RFLP, MSMSA
SNaPshot® primer focus kits
Custom Labeled Primer
5-FAM™, HEX™, NED™ (Dye Set DS-30 - Filter D) ROX™ GeneScan™ 500 ROX™ Size Standard Custom Fragment Analysis Custom Labeled Primer
6-FAM™, VIC®, NED™ (Dye Set DS-31 - Filter D**) ROX™ GeneScan™ 500 ROX™ Size Standard

Custom Fragment Analysis

Custom Labeled Primer
5-FAM™, JOE, NED™ (Dye Set DS-32 - Filter F) ROX™ GeneScan™ 500 ROX™ Size Standard
Microsatellite (Forensic)
AmpFℓSTR® Kits,
Plant/Microbial AFLP Kits®
6-FAM™, VIC®, NED™, PET® (Dye Set DS-33 - Filter G5) LIZ® GeneScan™ 600 LIZ Size Standard v2.0
Microsatellite (Forensic)
Custom Fragment Analysis
AmpFℓSTR® Kits,
Custom Labeled Primer
Capillary Electrophoresis

During capillary electrophoresis, the products of the PCR are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the fluorescent DNA fragments are separated by size and are detected by a laser/camera system.

Which Electrophoresis Instrument (Genetic Analyzer) Is Right for You?

Number of Capillaries96482481641
Compatible Applications:
(S) Supported; (A) AB Demonstrated; (C) Customer Demonstrated; (N) Not Supported
- GenotypingSSSSSSS
- Analysis for Forensics/HIDNNSSSSS
- Instability/RERAAAAAAA

Analyze the microsatellite profile. Appearance of numerous extra alleles in the microsatellite profile indicates a genome instability.

Which Data Analysis Software Is Right for You?

Highlighted products for ISSR Analysis:

Verti Thermal Cycler

3500 Series Genetic Analyzers

GeneMapper® Software