I have tried it, but (IMHO) it lacks Inkscape's flexibility.

very well said @probabilityislogic . Actually we talked about this in a recent class, and what you say is true.

Dr. Broman, I was just adding to your statement (nothing else)

ANOVA's F test is a generalization of the two sample t-test to cases with more than 2 treatments.

I think your problem is very solvable, but we need to understand your data better. Let's see if I understood you correctly: i. there are three factors (trt) of interest -- development, region, and genotype. ii. there is a batch effect also, about which you don't care. iii. I still don't understand the design (confusing to me at least). Could you tell us in plain English what is your experiment, how do you go about measuring the variables of interest, and how does batch effect creep in. Given this info, modeling will follow.

In your specific setting, the answer is YES. But in general the answer, I would say, is NO because continuous variables can vary according to groups. For example, income of residents in city should be higher than village (according to you this might be two separate categorical variables for location).