How to describe the relation between a course instructor to his teaching assistant?
It sounds like the question is that you need to fill in the "In what context have you known the applicant" box on a PhD recommendation letter.

If this is the case, then, for this particular point, I would not list "research supervisor," since this is clearly a teaching situation. However, "student" also doesn't make any sense. So, if there's no specific option which clearly satisfies this, I would check off the "other" box, fill in "teaching supervisor," and then explain the relationship clearly in the text of the recommendation letter itself.