In my research project, I have mentioned the use of RAPD and RFLP. But after some time I faced some problems with doing RAPD and RFLP. So Can I replace RAPD and RFLP test with ITS region Sequencing? Please suggest me.
Hi
You can use any technique other than RAPD and AFLP for diversity studies. But what are your samples? If they are species, ITS may be useful, but if the samples are below species levels (genotypes, cultivars) ITS sequence may give you less or no polymorphism? Assess this aspect before going ahead
Lakhan Yadav When you use RAPD/RFLP, you estimate the diversity of arbitrary genetic markers in the compared genomes (sure, the number of polymorphic non-correlated RAPD/RFLP loci must be large enough for reliable results). Sequencing the ITS, you estimate the diversity of a single intergenic fragment only. It could be no/only low correlation between these two methods.
I subscribe the answers from Alex Ignatov and Ajay Saini. Since you have technical posibilities to perform the above mentioned techniques, I would suggest the use of SSR markers. Microsatellites cover all the disadvantages of using either RAPD, RFLP and ITS, offering further benefits, eg are codominant markers highly reproducible allowing to compare results from different labs
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