Hi
We are presently working on molecular characterization of apples. After running gel we have got multiple bands with specific molecular weight. I am confused how should I perform my scoring. Can any one assist me.
Hi Sumira,
some SSR markers can result in the stuttering of DNA polymerase during PCR amplification. Are you doing genetic mapping using a population of apples? If so, just keep the various bands in the gel into account When looking at polymorphisms. A difference of at least one of the bands indicate polymorphism Between two genotypes.
@ Gundi thanks sir for reply. Sir, we are looking for genetic variation among 108 genotypes of Apple. Does stuttering create discreet bands. How should we score them as multiple band or single band.
Dear Sumira,
you will get one or two bands from SSR
please look to my papers
https://www.researchgate.net/profile/M_El-Sayed2/contributions
Hi Sumira,
I am not quite sure I understand right. You say that you have more than two distinct bands in a diploid organism? That should not happen, unless your primer pairs are not quite specific enough. The mentioned stuttering occures quite often, but that just creates a kind of "laddering" effect right around the "real" band. Do you run gels or are you using a sequencer? Could you post a picture so we could understand your problem better?
Regards,
Klaus
@Klaus it is not laddering effect but four band against specific primer and tomorrow I will post pic and yes I am running gel not sequencer.
Hi Sumira,
sorry for my late reply - I just now saw your post. Do you get those 4 bands consistently? That should not happen. Even if you have multiple target loci for this primer or even if you have an unexpected tetraploid one would expect a varying number of allels in a population. How about posting a picture of the gel?
Regards,
Klaus
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