Analysis of AFLP Assay dataEnlarge Image
Figure 1: Click to enlarge.

AFLP® is a technique used to detect polymorphisms in DNA when no information about the genome is known. Following restriction enzyme digestion of DNA, a subset of DNA fragments is selected for PCR amplification and visualization. A unique fingerprint is generated for a particular genome. AFLP®, first developed for plant studies, is now used for a wide variety of genetic analysis applications.

Figure 1. Analysis of AFLP® assay data from the P1, P2, and F1 samples. Plots on the left contain the AFLP® peaks (blue) and size standard peaks (red) for the three samples. The plot on the right side shows the bins (gray bars) and allele calls.

The power of AFLP® analysis is the speed with which the technique can quickly generate large numbers of marker fragments for any organism, without the need for any sequence data.

Step-by-Step Guide to AFLP® 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

AFLP analysis

Cut genomic DNA into fragments with the restriction enzymes Msel and EcoRI and Ligate adaptors.

Recommended Products: Perform Restriction digestion and Ligation

Which Products are Right for You?


Recommended Products: Perform PCR

Products Learn More
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
Fragment Length Polymorphism

Analyze the AFLP profile.


Recommended Products: Data Analysis

Highlighted products for ISSR Analysis:


New Capillary Electrophoresis Instruments Support Center
Find tips, troubleshooting help, and resources for support related to your capillary electrophoresis instruments.

Fragment Analysis Software Support Center