Maybe very light layers of fabric paint! However that might not be opaque enough. You could also try paint pens, but test a few brands out on rolled up paper first, to make sure you like how the paint sits after it's been rolled and unrolled a few times. Your biggest concern with most paints is it peeking/flaking off. Basic craft paints seem like a bad idea because they tend to be very flaky. Oil paint works really nicely on smooth surfaces like glass, I've found, so that could be an option, but it takes a very long time to dry, and I'm not experienced enough with it to say how it might behave once dry and rolled up.