As you can see above, the Advanced Menu Properties are hidden under the Screen Options pull down tab located in the upper-right corner of WordPress Dashboard.
NOTE: Make sure that you are in the Menus screen: http://yoursite.com/wp-admin/nav-menus.php
W.r.t your question, the Link Relationship (XFN) option is what you want “check”. Then the appropriate field will show up for each menu item allowing you to define its relationship (rel="____"). You can also leave it blank for some items (meaning, no relationship will be specified).
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