Since you said that you think there was a thunderstorm recently, your plants may have died because lightning struck your crops. From this thread:
Lightning storm could of struck the crop?
It is most probably a lightning, because it has just happened to me.
I still dont have rods and a day after a terrible two day storm one of my crops its just dead.
In order to prevent this, you'll need to build a lightning rod somewhere on your farm. It's worth noting that this won't completely protect your crops (apparently prior to build 1.07, they did virtually nothing to help).
The exact placement of the rod on The Farm has no bearing on the chance to intercept a lightning strike, rods do not protect a specific area. They have about a 50% chance to be struck.
As of patch 1.07: Lightning is more likely to strike trees than crops, but a Lightning Rod now has a very good chance of intercepting lightning strikes (if they aren't already processing a lightning bolt) It is also not necessary to be on the farm while the lightning strike happens.
As an aside, you can tell that it wasn't due to crows, as they will eat your crops, not leave a dead one.