Anoop Singh It is a usual result for RAPD primer with too many annealing sites in the genome of your plant, or annealing temperature is too low. You need to take 2-3 other primers. You can try higher Ta as well with this primer.

Dear Anoop Singh !

Can you upload a gel picture, so that we can see the smearing?

I attach you a trouble shooting guide from ThermoFischer. It helped me a lot to improve my PCR.

https://www.thermofisher.com/hu/en/home/life-science/cloning/cloning-learning-center/invitrogen-school-of-molecular-biology/pcr-education/pcr-reagents-enzymes/pcr-troubleshooting.html

Just a few recommendations:

* Your DNA quality is fine? What was the amount of your DNA you are using (ng/g)?

* How about your primer quality? I would lower a bit the primer concentration, for me the 2 uL seems to be a bit high.

* Too high level of Mg can also cause smearing.

* I agree with Alex Ignatov , changing the Ta could also help. Consider Touchdown PCR as well to enchance specifity.

* How many cycles did you use?

* Gel running conditions:

improperly prepared gel

if you used an old buffer, prepare a new one and change it, and also avoid too high voltage (100 or 110 V should be enough).

I hope I could give you some ideas.

Best regards,

Zsófia

often ,such smear formation appear when the DNA sample is not pure,It may not be the only reason too .