1. make sure your fit is right. too much or too little reach can hurt your back.
a. too little reach gives you a cramped posture and puts more weight on your saddle, and thus your lower back.
b. too much reach makes you bend over farther. it generally does reduce weight on your saddle, though. so maybe you shouldn't do this and instead...

2. increase your flexibility
a. do some light, gentle stretching before rides.
b. if you stop for more than 2 minutes mid-ride, more gentle stretching.
c. when you're totally done riding, do some GOOD stretching. do not wait until after you drive home. even if you don't see anyone else stretching, do it. who gives a crap what anyone else thinks.. it's your body.

3. get out of the saddle when going over rough terrain like roots and rock gardens. I bet you're doing this one already. don't stand rigidly, use your legs and arms as shock absorbers.