ISSR problems

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Anna.Schwabe's picture
ISSR problems

Does anyone have extensive experience with ISSRs? GeneTools by SynGene? GelCompar II?

I am doing population genetic work with 2 different plant species and i am using plate based PCR for both projects. In both projects, the data is grouping strangely.

I am running 96 samples (a whole plate) on one gel per plate. From some of the analyses I have run, it is obvious to me that the genetic groups resolving are acually an artifact of each plate, not genetic differences.

I have tried multiple things to try to elimnate this plate artifact and am at my wits end. Has anyone else had this issue? Any ideas of how to go about processing these data that may produce more accurate results?

ANy help would be appreciated.