Transposons as genetic markers Transposons may be used as genetic markers because they change the pattern of restriction fragment analysis (i.e. the results of analysis of DNA fragments obtained after digestion with specific restriction endonucleases). For instance, with the help of a probe, it was possible to characterize different strains of Plasmodium falciparum the causative agent of human malaria. Such identification of strains, which differ due to distribution of transposable elements, could be useful to clinicians and epidemiologists who may be interested in locating the source of a particular strain of the parasite. Transposons, which change the pattern of restriction fragment analysis, may also be used as genetic markers to construct linkage maps. These have also been used in humans for distinguishing carriers from non-carriers of disease like sickle cell trait. A set of cloned DNA fragments containing copies of transposons, should also contain unique sequences from specific regions of the genome and can be used in such studies.

Transposons as mutagens and transposon tagging for isolation of genes
Insertion of transposons can be used as a method for inducing mutations as has been shown in a number of spontaneous mutations like Ac-Ds system in maize, and P-M and I-R systems of hybrid dysgenesis in Drosophila melanogaster. Transposons usually cause mutations due to insertion in structural or regulatory region, rather than due to addition, deletion or substitution of bases. Therefore, these mutations can be used for a study of structural and regulatory regions of a gene. Further, a probe carrying a transposon can be used to screen the restriction fragments containing the mutant gene. This feature of transposons has also been utilized for isolation of genes though transposon tagging (see Genetic Engineering and Biotechnology 3.  Isolation, Sequencing and Synthesis of Genes). Several loci including white, scute and cut genes have been cloned in Drosophila melanogaster due to the presence of copia or gypsy elements described earlier.

Transposons as transformation vectors
This aspect of gene transfer technology will be discussed in more detail in Genetic Engineering and Biotechnology 3.  Isolation, Sequencing and Synthesis of Genes and Genetic Engineering and Biotechnology 4.  Gene Transfer Methods and Transgenic Organisms. However it has been shown that genes can be transferred artificially if carried by a transposon in a plasmid. For instance, a fragment of DNA carrying rosy gene within a P element was transferred in a plasmid, which was injected into embryos of a strain of Drosophila melanogaster, homozygous deficient for the rosy gene. It was found that 50% of the progeny did carry rosy⁺ progeny indicating successful transfer. There are also other examples in Drosophila of such successful transfers.

Ac and Ds elements can also be used in a manner similar to the one described above in Drosophila. This will be particularly useful, since at present the commonly used vector for higher plants is only Ti plasmid of Agrobacterium tumefaciens, which can be used conveniently only with dicotyledonous plants. Only after 1985, success in transformation of monocots was achieved through direct DNA injection or DNA bombardments using particle gun (see Genetic Engineering and Biotechnology 4.  Gene Transfer Methods and Transgenic Organisms for more details).