If number of bands(fragments) per individual using ssr marker is more than two what would be the reason?
One answer could be that your primers or your PCR conditions are not specific enough and amplify another sequence. It may happen if you work with polyploids (with similar parental ancestors) or in case your target is in conserved and/or repeated regions of the genome.
If the numbers of fragments are 3,4, or even five, this could be due to higher ploidy levels resulting from different sources. For example Rosa damascena is a tetraploid hybrid of two rose can yield upto to four bands (this is just an example and not the factual results).
Or you can also get the variable number of fragments if the primers are not right or there are some problems with the PCR conditions.
Reagrds
Anil
Thank you for your answers....Though my samples are diploid but still getting many bands for co dominant marker but in some specific primer not all..i repeated pcr 2-3 times still getting same result.
OK, so you can try to increase the Tm of your PCR in order to increase binding specificity (it works sometimes) or redesign your primers.
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