I ran an agarose gel with 8 fungal isolates to check the polymorphism. I am not sure if I can consider the marker with the missing band as polymorphic?
No, because you are not sure if the missing band is due to PCR inhibitors in your gDNA in this specific sample..
Gel image and run also not very clear but I think yes. Better you run on high concentration of agarose and on slow voltage its will show you clear polymorphism. All the best.
Thanks everyone. this is a 3% agarose gel and 45 V. What you suggest the gel concentration and voltage should be ?
Also, are 8 isolates enough to test for polymorphism? I will be using these SSRs for diversity study.
I think you can consider that marker as polymorphic due to a missing band/null allele. Also, confirm whether the DNA sample anneals with another marker..
Maybe they are but it isn't well distinguished with agarose. Even with the fragment sequencer might be difficult. You should sequence it and see if it is posible to find a cut point.
and regarding the missing one... try again.
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