Canonicals from sub-domain to main domain: How much content relevancy matters? Any back-links impact?

[vtmoz]

Hi Moz community,

I have this different scenario of using canonicals to solve the duplicate content issue in our site.

Our subdomain and main domain have similar landing pages of same topics with content relevancy about 50% to 70%. Both pages will be in SERP and confusing users; possibly search engine too. We would like solve this by using canonicals on subdomain pointing to main domain pages. Even our intention is to only to show main domain pages in SERP. I wonder how Google handles it? Will the canonicals will be respected with this content relevancy? What happens if they don't respect? Just ignore or penalise for trying to do this?

Thanks