Drupal - How to apply the attribute "rel=nofollow" to links in the comments?

Go to Configuration -> Content authoring -> Text formats -> Plain text (your format), then tick the Limit allowed HTML tags option.

In the filter settings at the bottom of the page is the Add rel="nofollow" to all links checkbox. Tick that... Since this is plain text, you will probably want to remove the contents of the Allowed HTML Tags field, too.