Is due to the repetitive sequences or any other reasons? Why these universal markers will give different banding pattern in different plants?How the pattern should justify the polymorphic Index ?
See:
PLoS One. 2016; 11(4): e0152972.
Published online 2016 Apr 12. doi: 10.1371/journal.pone.0152972
Theor Appl Genet (2002) 104:845–851 DOI 10.1007/s00122-001-0848-2
I hope this helps!
Check the following video for ISSR
Inter simple sequence repeats (ISSR)
https://www.youtube.com/watch?v=AVjUfXqKv7E
For RAPD
''the primer is short (e.g. 10-mer), there is a high probability that the
genome contains several priming sites close to one another that are in an inverted orientation. The technique essentially scans a genome for these small inverted
repeats and amplifies intervening DNA segments of variable length. The profile of amplification products depends on the template primer combination and is reproducible for any given combination. The amplification products are resolved on agarose gels and polymorphisms serve as dominant genetic markers, which are inherited in a Mendelian fashion''
If you have patience check my Answers link I answered many questions reg. RAPD in the very beginning, you get all answers for your doubts (I mentioned this earlier no idea whether you searched or not).
Primers are short and they are not specific to one site. Probably the genome contain more of that sites or repeats.
RAPDs primer anneal at multiple locus of the genome and more loci will amplify from a single RAPD marker and same as so in ISSRs
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