I am doing a diversity analysis of sugarcane germplasm. I did SSR. When I am running PCR products in PAGE the ladder and samples are not open properly. I apply 40w and run 2 1/2 hrs in 6% PAGE gel with 1x TBE. But in 2nd gel I run same set of samples in PAGE with urea. In this gel samples and ladder open properly but handling of gel is difficult. Bands are not clear as previous. In some papers they mention PAGE with urea. But in some references mention PAGE without urea. please advice me which one is the most suitable for me.
I have always used PAGE with urea for SSR analysis, i have undestood that it is important to use denaturating gels in these cases...
I previously worked with PAGE for diversity analysis in a set of rice germplasm. I used PAGE without urea. The bands were good. However, according to your attached pictures, it looked like the usage of urea is better off than without urea. If I were you, I'll stick on with the method that produce better results. Good Luck.
No need to use urea, if you want to use urea, PCR product should be denatured again to make it single strand. But you will get same result in urea-PAGE or without urea.