I extracted total RNA with the kit. When tested with Nanodrop, the quality was very good, but the concentration was very low. What could be the reason?
this is hard to tell as you don't give information about the material you used for extraction, the amount of material you used and which kit you used for extraction.
Maybe you could give some additional information to come up with some ideas why the concentration is low (what concentration did you measure)
Regarding the quality of your RNA - you can have good looking results from your Nanodrop regarding purity, however the RNA can still be more or less degraded.
So to see if you really have good quality RNA do a gel electrophorsis. For good quality RNA you should see two clear band (28s and 18 RNAs) - if you don't see them it might indicate RNA degradation.
I would do this always before subsequent application, because it can save you a lot of work (and also material) if the RNa quality is insufficient due to degradation.