Individual Analysis of Transposon Polymorphisms by AFLP

The DNA polymorphisms caused by insertion and excision of transposable elements (TEs) are applicable in studying genome dynamics, genetic diversity, and molecular evolution, generating genome-wide molecular maps and investigating functional attributes of transposons in epigenetics and diseases. Identification of individual mutations caused by TEs using the principles of amplified fragment length polymorphism assay is a reliable and cost-effective approach. The method relies upon selective polymerase chain reaction (PCR) of flanking regions of TE insertion sites in the genome. A detailed procedure is described in this chapter that outlines each step starting from the preparation of PCR template to identification and isolation of the polymorphic bands. The approach outlined in this protocol can be adopted to identify individual polymorphisms caused by any transposon in any organism.