It is short for "What classes are you taking?"

'taking' in this context means 'doing'. "What are you taking in college" is a general question on what studies you are doing. It could be asking what specific course or program you are doing, but as well it may be more generally asking what area of study you are doing. For instance, if I was doing a maths or computer science degree, I could answer the question by saying, "I'm doing maths and computer science". Or, I could be more specific in my response and give the exact title of the degree "I'm doing a degree in applied science".

I’m from the U.S., not Canada, and that question is a little weirdly phrased. I would interpret it as “What classes are you taking?” in which case “taking” means enrolled in (a class). It could also be interpreted as “What major are you in,” but in U.S. English, that would more commonly be phrased as “What are you studying?” My recommendation is to ask what the person means by their question! Then you’ll know for certain

Usually people ask "what's your major?" or "what are you majoring in?" when they want to know your major. "Taking" usually refers to which classes you are taking. Ex. "What are you taking in college?" "I'm taking classes in biology and chemistry this semester."