How do I change default keyboard layout (not input method) in Ubuntu 16.04?

In a shell:

sudo dpkg-reconfigure keyboard-configuration

I'm not able to reproduce the problem you have mentioned in comments, i.e. that enabling a Japanese keyboard layout wouldn't make a difference. I added Japanese, and the resulting keyboard layout looks like this:

Then I opened gedit, switched to "Ja" via the input source indicator, and the expected characters according to the image above appeared when I typed.